The fiddler crab Austruca occidentalis is a dominant species in mangrove forests along the East African coast. It enhances soil aeration and, through its engineering activities, makes oth- erwise-inaccessible food available for other marine organisms. Despite its importance, the hab- itat of A. occidentalis is threatened by human activities. Clearing the mangroves for salt farming and selective logging of mangroves trees continue to jeopardise mangrove ecosystems in the Western Indian Ocean. This study aims to use partial mitochondrial COI gene sequences and nuclear microsatellites to determine whether salt farming activities in mangroves have a nega- tive impact on the genetic diversity and gene flow of A. occidentalis collected along the Tanza- nia coast. The level of genetic diversity for both mitochondrial DNA and nuclear microsatellites are relatively lower in samples from salt ponds compared to natural mangrove sites. Analysis of molecular variance (AMOVA) among all populations showed low but significant differentia- tion (COI: Fst = 0.022, P < 0.05; microsatellites: Fst = 0.022, P < 0.001). A hierarchical AMOVA indicates lower but significant genetic differentiation among populations from salt ponds and natural mangroves sites (COI: Fct = 0.033, P < 0.05; microsatellites: Fct = 0.018, P = < 0.01). These results indicate that salt farming has a significant negative impact on the genetic diver- sity of A. occidentalis. Since higher genetic diversity contributes to a stable population, restoring the cleared habitats might be the most effective measures for the conservation of genetic diver- sity and hence adaptive potential to environmental change in this species.