6 Best Hatching Egg Marking Pens For Identification That Won’t Harm Embryos
Safely identify hatching eggs for better tracking. Our guide reviews 6 non-toxic marking pens that provide clear labels without harming developing embryos.
You’ve just loaded the incubator with a precious clutch of eggs from three different chicken breeds, all laid on different days. Now you need a reliable way to tell them apart for candling and tracking hatch rates. Before you grab the nearest marker, remember that an eggshell isn’t a solid barrier; it’s a porous membrane that can absorb whatever you put on it.
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The Importance of Safely Marking Hatching Eggs
An eggshell breathes. It has thousands of tiny pores that allow for the exchange of oxygen and carbon dioxide, a process vital for the embryo’s survival. Anything you write on that shell has the potential to seep through those pores and come into contact with the developing chick.
This is why choosing the right marking tool is not a minor detail—it’s a critical step in successful incubation. Using a marker with toxic solvents, like a standard permanent marker, can introduce chemicals that may harm or even kill the embryo. The goal is to make a clear, lasting mark for your records without compromising the health of the hatchling inside.
Get precise and bold lines with this 6-count Sharpie permanent marker set, featuring fine, ultra-fine, and chisel tips. The quick-drying, fade and water-resistant ink marks permanently on most surfaces.
Proper marking allows you to track fertility, monitor development during candling, and identify which eggs belong to which breed or hen. You might mark one side with an "X" and the other with an "O" for manual turning, or simply jot down the lay date. Whatever your system, it only works if the tool you use is 100% embryo-safe.
Ticonderoga #2 Pencil: The Classic Safe Choice
The simple #2 pencil is the old-school, tried-and-true standard for marking hatching eggs, and for good reason. The "lead" is actually a mixture of graphite and clay, both of which are inert and non-toxic. It poses zero chemical risk to the developing embryo.
The biggest advantage is accessibility and cost—you almost certainly have one lying around right now. It works perfectly for writing dates, breed codes, or turn indicators directly on the shell. It’s a simple, effective tool that gets the job done without any fuss or worry.
The main drawback is that graphite can be difficult to see on dark brown or blue eggs, like those from Marans or Ameraucanas. It can also smudge, especially in the high-humidity environment of an incubator. Wiping away condensation or handling the eggs for candling can sometimes blur your markings, so you may need to reapply them carefully.
Brinsea Incubation Marking Pencils for Eggs
If you like the safety of a pencil but want something designed specifically for the job, Brinsea’s marking pencils are a solid upgrade. These are essentially specialized grease pencils, but they use a non-toxic formula that is completely safe for eggs. They are built for this exact purpose.
Their key benefit is visibility. The marks are much darker and clearer than a standard graphite pencil, showing up well on almost any color of eggshell, from white Leghorn eggs to dark Welsummers. They are also more resistant to smudging in the humid incubator environment, ensuring your records stay legible for the full 21-day cycle.
Of course, this specialization comes at a higher price point than a box of #2 pencils. For someone hatching a few dozen eggs a year, it might feel like an unnecessary expense. But for those running a larger operation or simply wanting a more reliable, purpose-built tool, they offer a level of convenience and performance that justifies the cost.
Incu-Bright Egg Marking Pens: Designed for Safety
For those who prefer the feel and flow of a marker, the Incu-Bright Egg Marking Pen is a fantastic, safe alternative. This pen uses a non-toxic, alcohol-free ink that is specifically formulated to not penetrate the eggshell. It dries quickly and leaves a vibrant, easy-to-read mark.
The primary advantage here is the sheer convenience and clarity of a felt-tip pen. It glides smoothly over the egg’s surface, making it easy to write small, detailed notes without applying much pressure. The ink is bright and highly visible on all shell colors, which is a huge plus when you’re trying to quickly identify eggs in a full incubator.
While they are proven to be safe, they are a specialty item and can be harder to find than a pencil. They also cost more. Think of them as a modern solution for a classic task—perfect for the hobbyist who values precision and is willing to invest in a tool designed to make the process smoother and more reliable.
Crayola Crayons: A Non-Toxic, Colorful Option
Don’t overlook the simple crayon, especially those made by Crayola. Because they are designed for children and are required to be non-toxic, the wax formula is perfectly safe to use on hatching eggs. The wax sits on the surface of the shell and doesn’t pose a threat to the embryo.
The biggest benefit of crayons is the ability to color-code your eggs. You can use a different color for each breed, lay date, or breeding pen. This visual system can make sorting and tracking much faster than reading small letters or numbers, especially in a dimly lit room during candling.
However, there are tradeoffs. The wax can be prone to melting or rubbing off in the warm, humid conditions of an incubator. A mark that was clear on day one might be a waxy smudge by day 18. For this reason, crayons are best for simple marks, like a single dot or a stripe, rather than detailed numbers that could become illegible.
General’s Charcoal Pencils for Smudge-Free Marks
For a solution that combines the safety of a pencil with the boldness of a marker, consider a charcoal pencil. General’s is a well-known brand, and their pure charcoal pencils are an excellent choice. Like graphite, charcoal is an inert, carbon-based material that is completely non-toxic.
The advantage of charcoal over graphite is the dark, rich line it produces. It’s highly visible on nearly all egg colors, even dark olive and deep brown. More importantly, charcoal tends to smudge far less than graphite, especially once it has set on the shell’s surface. This makes it a more durable option for the 21-day incubation period.
You’ll likely need to find these at an art supply store rather than your local office supply shop. They behave much like a regular pencil but offer a significant boost in performance and legibility, making them a favorite for serious poultry keepers who want clear, lasting marks without any chemical risk.
FooDoodler Food Coloring Markers for Hatching
Another excellent and completely safe option comes from the world of cake decorating: food coloring markers. Brands like FooDoodler use FDA-approved, edible ink, the same kind used to write on cookies and cakes. If it’s safe to eat, it’s certainly safe for an eggshell.
These markers offer the best of both worlds: the convenience and brightness of a pen with unquestionable safety. They come in a variety of vibrant colors, making them perfect for complex color-coding systems. The marks are clear, dry quickly, and are easy to apply.
The only potential downside is that some food-grade inks may fade slightly over three weeks in a high-humidity environment. However, they typically remain more than legible enough for identification purposes. They are a brilliant, worry-free solution that brings a bit of color and certainty to your hatching process.
Markers to Avoid: Sharpies and Toxic Chemicals
This is the most important rule of marking eggs: never use a standard permanent marker like a Sharpie, a dry-erase marker, or a highlighter. These markers contain volatile organic compounds (VOCs) and other chemical solvents like xylene and toluene.
These harsh chemicals are designed to penetrate surfaces to create a permanent mark, and an eggshell is no exception. The solvents can easily pass through the shell’s pores and harm the delicate vascular system and embryo developing inside. Even the fumes can be toxic in the enclosed space of an incubator. Using one is a gamble that can lead to developmental defects or a failed hatch.
There is a lot of conflicting advice online, with some people claiming they’ve used Sharpies without issue. But it’s an unnecessary risk when so many proven, safe alternatives exist. When the health of your future flock is on the line, there is no reason to choose a convenient but potentially lethal tool. Stick to pencils, non-toxic specialty pens, or food-grade markers to ensure a safe and successful hatch.
Ultimately, the best tool for marking your eggs depends on your budget and how you track your hatches. Whether you choose a simple pencil or a specialized food-grade marker, the guiding principle is always the same: safety first. By choosing a non-toxic option, you give every single embryo the best possible chance to develop into a healthy, thriving chick.
