1. Anthropic influence on the environment has caused extensive damage, with several species becoming vulnerable to extinction, such as Hippocampus reidi, the seahorse with the largest distribution area in Brazilian estuaries. For instance, in the Maracaípe River estuary, north-eastern Brazil, once a sanctuary for the species, this seahorse is now increasingly difficult to find.2. Recovery strategies for species threatened with extinction include the introduction of individuals from a demographically healthy population, or the captive breeding and subsequent release of individuals from the population at risk. This study evaluated the evolutionary potential and the best way to manage the recovery of the Maracaípe seahorse population.3. The genetic diversity of 30 adults and 99 juveniles of H. reidi collected in Maracaípe were compared with those of 29 adults from a nearby, demographically healthy population in Jericoacoara National Park, Ceará. Inter simple sequence repeat (ISSR) polymerase chain reaction (PCR) was used, amplifying 96 polymorphic fragments from the studied groups. 4. Adults and juveniles from Maracaípe had high diversity and low genetic differentiation. The neighbour-joining method, based on the number-of-differences model, revealed two clusters: one with adults and juveniles from Maracaípe; and the other with adults from Jericoacoara only. The most probable number of genetic groups (K = 2) was also obtained using Evanno's test, which was confirmed by STRUCTURE.The analysis of molecular variance showed that more than 30% of the differences occur between these two groups (Maracaípe and Jericoacora). The population differentiation observed between Maracaípe and Jericoacoarasuggests genetic incompatibility between the individuals in each area, and points to the risk of outbreeding depression. Therefore, a possible conservation strategy for the Maracaípe population is a native captive breeding programme and the release of offspring in this location, aiming at the demographic recovery of the population in the area.