Nekovalkyrja sometimes have distinctive facial markings. They are not tattoos but rather birthmarks encoded into the Nekovalkyrja's genetic sequence. In the early days of Nekovalkyrja production by PNUgen Corporation, these markings helped differentiate otherwise identical Nekovalkyrja clone soldiers.

Nekovalkyrja facial markings are typically blocks of color on the forehead, cheeks, or chin. The colors can run the whole spectrum of pigments and tend to either be bright colors or pastels. Pink and red are the most common colors.

Sometimes markings can extend onto or be duplicated onto other parts of the body like the back. One style is a line that runs over one eye and then down the entire body.