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Fisheries bycatch is one of the most significant marine conservation issues as valuable fish are wasted and protected species harmed with potential negative ecological and socio-economic consequences. Even though there are indications that the small-scale handline fishery of the Galapagos Marine Reserve has a low selectivity, information on its bycatch never has been published. We therefore assessed the bycatch of the Galapagos handline fishery by estimating the bycatch ratio, determining species compositions of landings and bycatch, and identifying fishers’ reasons for discarding certain individuals using onboard monitoring and interview data. Moreover, we used interview surveys to reveal historical trends in the bycatch ratio. The estimated bycatch ratio of 0.40 confirmed a low selectivity of this fishery. Characterisation of the catch resulted in a total of 19 target species which were dominated by groupers, and 53 non-target species, with grunts and groupers being most prominent. Most individuals were not landed for economic motivations, either because species (77.4%) or sizes (17.7%) are not marketable and to a lesser extent for regulatory reasons (5.9%). However, sharks were after grunts with 69% the second most often mentioned bycatch taxa during interview surveys. We found that small sized individuals of some of the most exploited species suffer high bycatch mortality because they are used as bait. Moreover, over half of interviewees perceived a historical decrease in bycatch ratios that was explained by a diversification of the catch composition due to the reduction in abundance of the traditionally most important target species. As some target species show signs of overfishing and to date there are no specific regulations for the finfish fishery in place, we recommend the investigation of different gear settings such as the use of different hooks and bait species. Furthermore, we suggest the integration of faster growing species to the local market as well as spatio-temporal closures, and minimum and maximum catch sizes for overexploited species in order to improve the selectivity and sustainability of the Galapagos handline fishery.