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The Acrothoracica are small, diecious barnacles burrowing into calcareous substrata such as mollusk shells, corals, bryozoans, thoracican barnacles or limestone and calcareous chalk. They represent the most generalized group within Cirripedia and have featured prominently in phylogenetic speculations concerning these crustaceans. Traditionally, two orders the Pygophora and Apygophora were recognized for the Acrothoracica. The Apygophora had uniramus cirri and lack an anus, whereas Pygophora had biramus terminal cirri and an anus and was further divided into two families, the Lithoglyptidae and Cryptophialidae. Recently the phylogeny of the Acrothoracica was reconstructed on the base of numerous morphological traits of adult and larval stages and they were rearranged into two new orders, the Lithoglyptida and Cryptophialida (Kolbasov, 2009). The Lithoglyptida consists of the families Lithoglyptidae and Trypetesidae those females have a wide aperture, large saddle like labrum and developed mouth cirri. The females of order Cryptophialida with monotypic family Cryptophialidae have bottle-shaped mantle sac with narrow necked operculum, elongated, tongue-shaped labrum, and reduced mouth cirri. Logically, the studies of molecular genetics of the Acrothoracica are necessary to complete these works. We collected 25 species from 7 genera of orders Lithoglyptida and Cryptophialida for molecular analysis. We used molecular techniques to resolve the systematics of the acrothoracican barnacles, using the mitochondria DNA, COI, 16S region and the nuclear marker 18S and histone 3 region. The resulting phylogenetic tree of the Acrothoracica supports the recent taxonomic arrangement in Kolbasov 2009 and provide insight into the evolution pattern of different morphological characters of acrothoracican barnacles