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 Pinnixa White, 1846 sensu 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 franciscana Rathbun, 1918, Pinnixa littoralis Holmes, 1894, Pinnixa schmitti Rathbun, 1918, and Pinnixa tubicola Holmes, 1894 are placed in the genus Scleroplax Rathbun, 1893, whereas Laminapinnixa miamiensis McDermott, 2014, Laminapinnixa faxoni (Rathbun, 1918), Pinnixa abbotti Glassell, 1935, Pinnixa arenicola Rathbun, 1922, Pinnixa floridana Rathbun, 1918, Pinnixa leptosynaptae Wass, 1968 and Laminapinnixa vanderhorsti Rathbun, 1924 are reassigned to Glassella Campos & 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 pearsei Wass, 1955 – Pinnixa sayana Stimpson, 1860 complex, Pinnixa affinis Rathbun, 1918, and species in the Pinnixa californiensis Rathbun, 1894 – Pinnixa occidentalis Rathbun, 1893 complex; Tubicolixa n. gen. includes Pinnixa chaetopterana Stimpson, 1860 and the Pinnixa brevipollex Rathbun, 1898 – Pinnixa rapax Bouvier, 1917 complex; and Sayixa n. gen. is established for Pinnixa monodactyla (Say, 1818).