||In an ecosystem approach to fisheries management (EAFM) framework of the tuna purse-seine fishery, the assessment of target species, but also that of bycatch species, is essential. In the Atlantic and Indian oceans, purse-seine nets are sometimes set around tuna schools associated with whale sharks and baleen whales, although less frequently than around free-swimming tuna schools or those associated with fish aggregating devices (FAD). However, knowledge on the targeted catch and bycatch in these megafauna associated fishing sets is still relatively limited. Therefore, the aims of this study were to assess species and size composition of the target tuna species, as well as the diversity of bycatch species in whale and whale shark associated sets. Whale associated sets were found to be very similar to free school sets in terms of tuna catch (large yellowfin tuna), bycatch occurrence (presence in half the sets) and species assemblage (alpha and beta diversity). Whale shark associated sets were intermediate between FAD and free school sets, with tuna catch (skipjack and juvenile yellowfin) closer to FAD than to free school sets. However, the presence of large yellowfin, the bycatch composition (with almost no finfish, abundantly captured in FAD sets) and the species assemblage showed similarity with free school sets. This study highlights the need for an EAFM in the tuna purse-seine fishery by providing knowledge on pelagic multi-specific catches and bycatches.