The Amazon River dolphin (Inia geoffrensis), or boto, is illegally harvested for use as bait in fisheries for the catfish Calophysus macropterus. To determine the effect of this harvest, we estimated apparent survival for a boto population in the central Brazilian Amazon where direct harvest is known to have occurred since 2000. For our analysis, we used capture and recapture/resighting data of 528 marked botos over a 17-year period (1994-2011). Time-dependent models estimated that apparent survival after the first reports of harvest (f=0.899; SE=0.007) was significantly lower than in years prior to harvest (f=0.968; SE=0.009). The decline in apparent survival suggests that current harvest rates exceed conservation limits and may be unsustainable. This issue requires the attention of natural resource managers from all countries of the Amazon basin, as the harvest is widespread and decline in survival could be mirrored in numerous locales.