ABSTRACT Hippocampus patagonicus is classified as endangered in the vulnerable category by Brazilian law (MMA, 2014), and by IUCN (International Union for Conservation of Nature) criteria. Thirteen boats from the commercial fishing fleet of southern Brazil were monitored for 17 months to supplement data for the evaluation of this species. Three seahorse collection points were established, where the fish are landed: port of Imbé/Tramandaí and port of Passo de Torres (northern coast (NC) of Rio Grande do Sul) and the port of Rio Grande (southern coast (SC) of Rio Grande do Sul). The presence of H. patagonicus was recurrent, and the collected animals were between 22 and 130 mm in height. The species was captured from 11 to 57 m deep as bycatch of significant transboundary marine resources (Brazil, Uruguay, and Argentine). In bycatch of gillnet fishing (NC), estimated capture was 0.68 ± 0.97 seahorses/month/vessel, annually, an average of 89.76 seahorses would be removed from the sea by the 11 vessels involved. In trawling (SC), it was 49.66 ± 64.86 seahorses/month/double-rig trawl. It is estimated that 8,342 seahorses are removed annually as bycatch, only in this mode of fishing. The information obtained reinforces the need to apply ecosystem management to fisheries for the recovery of stocks that are over-exploited and accompanying fauna as well, especially small species with poorly known life histories such as H. patagonicus.