Photo-identification and conventional tagging were used to estimate population size and structure of the whale shark Rhincodon typus near Holbox Island, Mexico. From 2005 to 2008, photographs of spot patterns behind the last gill slit and in a lateral view on the left side of each animal were used to identify individuals. Additionally, 578 R. typus were tagged using conventional marker tags. Of these and the 350 R. typus that were identified from 1184 photographs, 65% were male; 27%, female and 8%, indeterminate sex. Photographed R. typus ranged in size from 2·5 to 9·5 m total length. Size was bimodal with a large peak at 6 m and a smaller peak at 7 m. Photo-identification showed that there was considerable loss of marker tags. Few of these remained on the animals for more than a year, so that interannual re-sights using tagging could not be used in population modelling. Forty six interannual re-sightings were found in the photographic library; the interval between these re-sightings was typically 1 year. It was estimated that the R. typus aggregation near Holbox Island ranged from 521 to 809 individuals, based on mark–recapture models. From 13 to 33% of R. typus photographed had scars that were attributable to boat strikes. This study provides a baseline for assessing the status of R. typus near Holbox Island. This information is useful to understand drivers of local population size and distribution and potential concerns about increasing effects of tourism on R. typus in this area and for designing better management programmes for R. typus conservation.