Cryptic species and lineages have been widely reported during the last decades, particularly in the marine realm. Misidentifications and ignoring species complexes imply many consequences, notably biasing biodiversity and connectivity assessments, which in turn mislead our understanding of ecosystems and impact the effective design and management of conservation plans. Focusing on the Indo-Pacific coral genus Pocillopora, playing key roles in reef ecosystems as one of the main bio-constructors, we report the first Pocillopora PSH16 (ORF53; sensu Gélin et al. 2017) colonies (N = 19) in the Western Indian Ocean (Nosy Tanikely, Madagascar), 6000 km further from its current distribution. Colonies were identified according to their mitochondrial open reading frame (ORF) haplotype and Bayesian assignment tests based on 13-microsatellite genotypes. Additionally, we performed genetic structure and diversity analyses with sympatric colonies from other Pocillopora species and Pocillopora PSH16 colonies from the tropical southwestern Pacific, revealing (1) a weak clonal richness, (2) a weak genetic diversity and (3) a relative isolation for the newly reported PSH16 colonies. These colonies thus represent either a new, distinct and uncommon, genetic lineage or isolated remnants of a wider one. In any case, unless specific management measures are implemented, their long-term maintenance seems compromised due to restricted gene flow within a restricted pool of genes.