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This study aimed to evaluate and compare seasonal variations of Hippocampus reidi population structures in two Brazilian coastal areas. Samples were collected from the rocky shores of Urca and Duas Irmãs Island by freediving along fixed transects. All seahorses observed in the study were recorded, measured, and identified by sex and reproductive stage. Seahorse behavior and fish depth were also registered. All individuals were photo-identified to estimate recapture rates. Holdfast used by seahorses was also recorded. Results showed low densities at both sites; sex ratio and juvenile/adult proportion did not appear to vary with season. The seahorse height differed between the two areas but did not vary with season nor sex. Seahorses in both sites were found in shallow waters (i.e. up to 4 meters), and the depth did not vary by season nor sex. Males were more frequently recaptured than females in both areas. All seahorses were reproductively active year-round, peaking at rainy periods in both areas. The seahorses were more often recorded while resting and seemed to anchor on seaweed. Though in different bays, seahorse population structure and seasonality appeared similar. These data provide useful baseline data for future population assessments.