We made surveys for whale sharks Rhincodon typus on a total of 99 d from April through June each year from 2006 to 2008 along the southern fringe of the South Ari Atoll, Maldives Archipelago. We recorded the length and sex of each shark observed and made photographs to facilitate repeated identification from their spot patterns using pattern-recognition software. We identified 64 whale sharks from digital photographs taken during 220 sightings over 3 yr. Approx. 87% of those sharks were immature males. The average length of recognisable sharks was 5.98 m (range 2.5 to 10.5 m), significantly shorter than that reported for whale sharks in other aggregations in the Indian Ocean. Our findings suggest that these sharks are either a small proportion of a local population or perhaps an even smaller component of a regional population in the western Indian Ocean. We applied a Lincoln-Petersen closed-population mark-recapture model and a Jolly-Seber open-population model to estimate population size, but found that neither model provided reliable results because key assumptions of each were not met.