Bay-capped Wren-Spinetail is monotypic; there are no described subspecies. There is a low level of morphological variation, however, between populations in coastal salt marshes, and those resident at inland, freshwater marshes: the coastal birds have shorter and thicker bills, and darker dorsal plumage, than do birds of freshwater marshes (Cardoni et al. 2013). There is very little genetic divergence (based on assessements of mitochondrial DNA and of microsatellites) between coastal and inland populations, however (Cardoni et al. 2013).
Described as Synallaxis maluroides (d'Orbigny and Lafresnaye 1837), with a type locality of Buenos Aires, Argentina. The genus Spartonoica was proposed by Peters (1950), with maluroides as the type (and only) species.
The phylogenetic affinities of Spartonoica long have been unclear. Vaurie (1980) suggested that it was closely related to Synallaxis, whereas Hellmayr (1925) placed maluroides in Asthenes; Ridgely and Tudor (1994) maintained maloroides in Spartonoica, but agreed that it probably was more closely related to Asthenes than to Synallaxis. Phylogenetic analysis of DNA sequence data, from both mitochondrial and nuclear genes, indicates that Spartonoica is sister to the genus Pseudoseisura, and that Spartonoica + Pseudoseisura in turn are sister to a clade composed of Synallaxis and Certhiaxis (Derryberry et al. 2011).