Alpheus lobidens sensu lato is one of the most common groups of snapping shrimps in the Indo-West Pacific. The objective of this study was to investigate the phylogenetic relationships among lineages of A. lobidens s.l. throughout their geographical distribution and identifying possible morphological characteristics that support the lineages from this combined dataset. Molecular data were obtained by analysing 16S rRNA from nine individuals of A. lobidens, three of A. buckupi, one of A. inopinatus and six other Alpheus species. The genetic analyses (mean p-distance and Bayesian Inference) indicate considerable genetic divergence and at least nine lineages within the A. lobidens species complex. The high morphological variability observed in Alpheus spp. and the high rates of interspecific genetic divergence agree with the Marine Ecoregions of the World and ocean currents, which suggests limited gene flow among those lineages, indicating that these could be treated as new species. However, as no informative morphological characters were identified, describing the six new taxa of the complex recognised in this study was unfeasible. Future studies using a higher number of specimens and applying more sensitive methods for detecting structural differences, might help morphologically define the new species that were uncovered herein.