HMS is the Highly Migratory Species permit. It is a federal permit that is required if you plan on bringing home yellow or bluefin tuna (and others), some sharks such as threshers and mako, swords, billfish, and even dolphin so I'm told (although I didn't see that one in the books ::)).
Its just another way the feds get your $25. Actually I don't think its so much about the $25 as it is the money brought in from citations when they catch someone without it. You buy the permit for the boat, not the fishermen.
Its a bunch of BS if you ask me. :P My 2006 expires like today I think, so before I go again I have to renew.
Here is the link to the application:
http://swr.nmfs.noaa.gov/hms/hmsapp.pdf