The pokemon world is a diverse place, and many cultures have had different interpretations of what the markings on the Moon actually mean. To some they are men, to peoples at extreme latitudes cheese. Most commonly, they are said to represent a Nidorina, and therefore that pokemon is typically associated in myth with lunar deities, who are therefore considered female.
In reality, the markings could just as easily represent a Buneary, or perhaps a Nidorino or a Nidoran or even a Pikachu. But it is Nidorina who claims this title most often by far, for it is Nidorina who always seem to be staring up at the moon, waiting for a piece of it to fall to earth so they can evolve.
The origins of these mysterious moon shadows are still debated by astronomers, but current speculation holds them to be a sort of giant geoglyph, similar to the Pattern Bush in the Sevii Islands. Whether this means the Moon is dominated by men who worship Nidorina (or perhaps some similar-shaped pokemon) a society of Nidorina themselves, or something else far stranger is known only to its inhabitants and the Clefairy.