Background An aggregation of juvenile whale sharks were first reported off Arta, Djibouti, in 2003 and formally investigated in 2006. Standardised monitoring started in 2009 to establish the demographics of this aggregation and how it relates to the broader Red Sea and Indian Ocean whale shark population. Approach Photo-identification images have been collected from 2003 to present. Satellite relayed archival tags have been deployed to show longer term movements and tissue samples have been collected for DNA. Plankton and environmental information are routinely recorded. For the last two years digital Photo-IDs were collected by volunteers at the local dive operation to enable a longer annual study period to help establish seasonality and sighting trends. Results During 2003–2015, a total of 503 individual sharks were identified by photo-identification from more than 6300 in-water encounters; a maximum of 181 individuals were recorded in a single year. Overall 85% of sharks identified were males and mean body total length ranged from 3.5–4.3 m among years, with no significant difference between sexes. Sharks which were sighted in more than one year had a mean period of inter-annual residency of 4 years (maximum 11 years, n=3). Using data from 2003–2015, mark and recapture models estimated a gross population of 660–777 with 53–78% of individuals being re-sighted in any one year. Satellite tag data showed tagged individuals left the immediate area and travelled into the Red Sea and Northern Indian Ocean; however, 2 of the 3 PAT tagged sharks were seen off Djibouti in subsequent years. Diving depth data showed all sharks made short duration dives to depths greater than 400 m (maximum 832 m) but that all spent at least 45% of the time within 10 m of the surface and an average of 73% of the time shallower than 40 m. Comparison with plankton and environmental data showed that sharks were associated primarily with high plankton concentrations and swimming crab (possibly Charybdis erythrodactyla) spawning events. Conclusions The Arta area off Djibouti is host to a regular and significant aggregation of whale sharks. The average size of the sharks is smaller than those found in other Indian Ocean coastal aggregations suggesting that this may be an intermediate or kindergarten group from which the sharks will leave as they grow to join other juvenile aggregations. Satellite tracking and photo ID support the movement of sharks into Red Sea aggregations.