I think your concern is about the potential toxity of the ink and solvent to sea life. Sharpies (as a brand) use a "non-toxic alcohol based ink formula" (per their website). Unless you jump in immediately after using a marker, the solvent (alcohol) is going to be gone. The only concern then would be if the ink itself flakes off. As long as you don't write on a hard, very glossy surface, it's likely that the ink will have absorbed into the surface of whatever you wrote on enough that it won't flake off.
I actually would be more concerned by the paint pen approach suggested by some since the solvents tend to be more organic in nature and the paint itself could be more toxic. Again, if applied properly and well in advance of the dive, it shouldn't provide any imminent harm to fish life or the environment.
In reality, it's a question of "dose". If a few miniscule flakes of ink come off of one set of equipment, no harm, no foul. If there are 1,000,000 divers, each giving off a few flakes, it gets a little more serious. However, relatively speaking, there's more potential harm from all the nasty sunscreens that people slather on - that's why the parks in Mexico recommend bio-degradable sunscreens. Without doing the scientific research, I'd suggest that the risk of potential harm from using a Sharpie to mark your equipment is extremely low.
Looking at the thread provided by gfisher4792, you'll see that a lot of folks use "permanent" tags on some of their gear, but that doesn't always work well with items like fins. I've been a few boats where mine weren't the only pair of blue Oceanic Quattros, and I appreciated having my name on them when it came time to retrieve them from the post-dive scrum.