Fisheries bycatch is a significant marine conservation issue 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 has never been published. We used onboard monitoring and interview data to assess the bycatch of the Galapagos handline fishery by estimating the bycatch ratio, determining species compositions of landings and bycatch, identifying fishers’ reasons for discarding certain individuals, and revealing historical trends in the bycatch ratio. The estimated bycatch ratio as a function of biomass of 0.40 and a diverse species composition of target catch and bycatch confirmed the low selectivity of this fishery. Most individuals were not landed for economic motivations, either because species (77.4%) or sizes (17.7%) are unmarketable or for regulatory reasons (5.9%). We found that bycatch contributes to growth overfishing of some target species because they are discarded or used as bait before reaching their first maturity. Moreover, over half of interviewees perceived a historical decrease in bycatch ratios that was explained by a diversification of the target catch 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 species in place, we recommend the implementation of a series of management measures to protect critical life stages of overexploited species and to improve the selectivity of the Galapagos handline fishery.