Population size and structure of whale sharks (Rhincodon typus) remain unknown despite their economic importance to targeted tourism and fisheries and their 2002 listing on CITES Appendix II. Here, we present results from the first whale shark population study in the Western Hemisphere and describe the inherent difficulties of assessing populations using catch-independent methods in free-ranging sharks. From 1998 to 2003, we identified 106 whale sharks using their distinctive scars and spot patterns following 521 encounters at a predictable seasonal aggregation on the Mesoamerican Barrier Reef linked to snapper spawning aggregations at Gladden Spit, Belize. Encountered sharks measured a mean total length of 6.3m±1.7m S.D. and a range of 3.0–12.7m (n = 317). Sexual and size segregation is suggested: 31% of encountered sharks (n = 162) were sexed, of which 86% were immature males. Between 1999 and 2002, 70 sharks were tagged with 72 conventional tags and measured sharks (n = 63) possessed a mean length of 6.0m±1.6m S.D. (range 3.0–9.7 m).