Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of and reassignment of this species as comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.