Aim To investigate whether the populations of 17 widespread hydroid species are connected on a demographic level (one to few generations) or are mostly connected on evolutionary timescales. Location Coral reefs of the South‐western Indian Ocean. Taxon 17 widespread hydroid species (Cnidaria, Hydrozoa). Methods Using mitochondrial (16S) and nuclear (Calmodulin) sequences, we analysed 17 co‐distributed hydroid species with contrasting life history traits (with or without a pelagic life history phase). We used DNA‐based species delimitation methods, haplotype networks, analysis of molecular variance, and Bayesian skyline plots to investigate diversification and connectivity patterns in the region. Results Putative cryptic species were revealed in half of the species and the 17 species resulted in 54 cryptic lineages. The high isolation of hydroid populations in the region is underlined by the rarity of shared haplotypes among localities in most of the species studied. In contrast, haplotypes shared between specimens collected in different ocean basins were found in three species and suggest recent introductions via human activities. The presence of a short pelagic dispersal phase did not seem to increase the connectivity levels of the studied populations, as no significant differences in genetic structure were detected between species with contrasting life history traits. Main conclusions These results highlight once again our incomplete knowledge of the marine invertebrate fauna, as we might be underestimating hydroid diversity by two‐thirds, and are discussed in terms of diversification processes, dynamics of the Indo‐Pacific biodiversity and the role of its peripheral marine provinces.