I am an architect and just finished school a few years ago...as a result I have a lot of art supplies lying around that rarely get used these days. I dug out my marker collection today and made a few marks on a piece of scrap leather to see how well they marked the material. I was shocked at how well the markers worked and I even put the scrap under some hot water to see if the colors would bleed and they did not. I'm sure someone has done this before but I thought I would share. The markers I used were Pantone Tria brand and Berol Prismacolors. The darker markers really look good whereas the lighter markers don't show up as well.
You can pick up good art markers at your local art supply store. Another brand available is ChartPak...I try to steer clear of chartpaks for paper because they bleed so bad...just an FYI if you run across those at the store. Buy one and try it on leather...I bet it will bleed like a stuck pig just like it does on paper.
Hopefully this will help someone.