In the past 24 years, the Southwestern Indian Ocean (SWIO) region has lost about 4% of its mangroves due to unsustainable extraction, land clearance for agriculture and climate change impacts. Since this loss risks fragmenting mangrove fauna, this study analysed 179 D-loop sequences (329 base pairs) of Barred mudskipper (Periophthalmus argentilineatus) sampled from estuarine mangroves in the SWIO to test two hypotheses: (1) whether Barred mudskipper populations in the region display genetic connectivity along the fragmented mangroves and (2) whether these populations have experienced demographic declines in recent history. The populations showed low and insignificant indices of genetic differentiation (F_ST = −0.00068, p > 0.05; Φ_ST = 0.005, p > 0.05), and haplotypes from different localities did not cluster according to their geographical origins. Similarly, Bayesian phylogenetic analysis grouped all SWIO haplotypes into one cluster, suggesting the hypothesis of genetic interconnectedness could not be rejected. Furthermore, the populations showed high haplotype diversity (0.96 ± 0.007) combined with low nucleotide diversity (1.09 ± 0.61%). They also showed significant negative Tajima's D values (−1.71, p < 0.02) and a unimodal mismatch distribution, indicating the hypothesis of demographic expansion post a historical bottleneck could not be rejected. Nevertheless, the Bayesian skyline plot indicated an increase in population size post-bottleneck, suggesting an ongoing recovery. These findings indicate that, despite varying management approaches in the SWIO, Barred mudskipper populations exhibit genetic exchange that transcends geographical and administrative borders. This implies that their populations should be considered a single stock within the region. These findings underscore the need for coordinated management approaches among the SWIO countries. This is crucial because inconsistencies in conservation measures across borders could disrupt the population's interconnectedness, potentially impacting their genetic integrity and long-term survival.