The phylogenetic relationships of inshore squid species in the family Loliginidae is still ambiguous owing to the lack of morphological and molecular data. In the present study, the taxonomic status of squid species Uroteuthis duvaucelii (Orbigny, 1848), Uroteuthis edulis (Hoyle, 1885), Uroteuthis singhalensis (Ortmann, 1891) and Loliolus hardwickei (Gray, 1849) from the Indian coast was elucidated by performing both morphological and genetic analyses. These Uroteuthis species showed marked differences in arm sucker teeth among species. Sharpness of tentacular sucker teeth was slightly increased in the order U. edulis < U. duvaucelii < U. singhalensis. Sexual dimorphism in tentacular teeth was observed in L. hardwickei. Uroteuthis singhalensis is morphologically very close to U. duvaucelii, as inferred by similar shape (broad, squared) and number (5–9) of arm teeth. Bayesian phylogenetic analysis using mitochondrial COI (650 bp), Cyt b (900bp) and COI-Cyt b combined gene sequences re-established the concept of monophyly of Loliolini with the additional number of species U. singhalensis and L. hardwickei. Our reconstructed phylogeny strongly supports Uroteuthis as a paraphyletic taxon as all organisms belonging to the genus Loliolus, including L. hardwickei (subgenus: Loliolus) explicitly grouped with one of the Uroteuthis clades. Distinct subclades within U. duvaucelii and U. edulis from the Indian Ocean may represent cryptic species.