Cirripedes of the superorder Acrothoracica are normally found as epizoic borings on marine calcareous substrates. Armatoglyptes taiwanus (Utinomi, 1950) is a lithoglyptid acrothoracican barnacle reported from different parts of the Indo-Pacific. Recent studies have demonstrated phylogenetic breaks between the Indian and Pacific Oceans populations in widespread Indo-Pacific marine organisms due to isolation events during the Pleistocene glaciations. It is possible that A. taiwanus represents a cryptic species complex in the Indo-Pacific, which the previous studies have failed to identify from morphology alone. In the present study, we analyzed the morphology and the sequence divergence of the 12S rDNA of A. taiwanus from the Indo-Pacific region, including Taiwan and the Philippines in the Pacific, and Phuket Island (Thailand) and the Mozambique Channel in the Indian Ocean, to test whether A. taiwanus is a cryptic species across its geographical range. The results showed that A. taiwanus has a homogeneous population structure in Taiwan, the Philippines, and Phuket Island (sequence divergence < 1%). Specimens from the Mozambique Channel, although morphologically similar to A. taiwanus, have a greater sequence divergence of 9.4% from A. taiwanus in the Pacific, and thus appeared to represent a new species, described herein as Armatoglyptes flexuosus n. sp. Although both species are morphologically similar, A. flexuosus n. sp. has more strongly bent/recurved posterior processes of the opercular bars and feebler armament of the orificial knob than does A. taiwanus from Taiwan (type locality). Phylogenetic analysis showed that populations of A. flexuosus n. sp. from the Mozambique Channel and A. taiwanus from the Pacific region are indeed closely related. Populations of their common ancestor may have become isolated and underwent speciation during the Pleistocene glaciations.