Sandy beaches are predominant ecosystems in the coastal zone of Brazil. In the interstitial environment, several microscopic species called microbenthos are responsible for primary production, consumption of bacteria and decomposition processes. Ciliophora is one of the most diverse phylum within the microbenthos, although its diversity and ecological aspects are still underestimated. We selected 12 beach segments in the south coast of Bahia, northeastern Brazil, to verify the diversity and connectivity between open and extensive beaches and those isolated by rocky outcrops. We found 52 morphospecies distributed in 16 families of ciliates. Statistical analysis showed higher richness in open beaches when compared to isolated ones, that could be due to their extension area, low hydrodynamics and organic matter retention. Urbanization factor, when interacting with beach categories, affect ciliates species richness. In our samples, open beaches presented a higher number of ciliate families in comparison with isolated beaches, and urbanization seemed to influence these differences. Species composition analysis showed high connectivity of ciliate assemblages between the beaches sampled, without significant diferences. The diversity profile showed that open beaches have greater diversity in comparison with isolated beaches. Urbanization profiles did not show diferences in ciliate diversity. More studies on marine benthic ciliates diversity and their ecological aspects are needed to understand their distribution patterns and assemblage connectivity.