We used mitochondrial 16S-NADH1 complex, mitochondrial 12S, and nuclear histone 3 genes to infer a molecular-based phylogeny, which allowed us to study phylogenetic relationships between species of PinnixaWhite, 1846sensu lato and other closely related pinnotherids. Polyphyly of Pinnixa s.l. was confirmed by maximum likelihood analyses. By our restricted definition, the genus Pinnixa sensu stricto is represented in these analyses only by its type species, Pinnixa cylindrica (Say, 1818). As a result of these molecular analyses, in combination with morphological studies, twelve species are reassigned to existing genera: Pinnixa faba (Dana, 1851), Pinnixa franciscanaRathbun, 1918, Pinnixa littoralis Holmes, 1894, Pinnixa schmittiRathbun, 1918, and Pinnixa tubicola Holmes, 1894 are placed in the genus Scleroplax Rathbun, 1893, whereas Laminapinnixa miamiensisMcDermott, 2014, Laminapinnixa faxoni (Rathbun, 1918), Pinnixa abbotti Glassell, 1935, Pinnixa arenicola Rathbun, 1922, Pinnixa floridanaRathbun, 1918, Pinnixa leptosynaptae Wass, 1968 and Laminapinnixa vanderhorstiRathbun, 1924 are reassigned to GlassellaCampos & Wicksten, 1997, the last two strictly on morphological bases. In addition, three new genera are erected to receive nine species: Rathbunixa n. gen. includes members of the Pinnixa pearseiWass, 1955– Pinnixa sayana Stimpson, 1860 complex, Pinnixa affinisRathbun, 1918, and species in the Pinnixa californiensisRathbun, 1894 – Pinnixa occidentalis Rathbun, 1893 complex; Tubicolixa n. gen. includes Pinnixa chaetopterana Stimpson, 1860 and the Pinnixa brevipollexRathbun, 1898 – Pinnixa rapax Bouvier, 1917 complex; and Sayixa n. gen. is established for Pinnixa monodactyla (Say, 1818).