Phylogenetic relationships among members of the subtribe Abutilinae and particularly the taxa in the Sida generic alliance are currently poorly understood. The internal transcribed spacers of nuclear ribosomal DNA (ITS1 ITS2) from 58 species (51 new sequences) of Malvaceae were sequenced. The ITS data show that species from sects. Cordifoliae, Ellipticifoliae, Muticae, Sida, Spinosae, and Stenidae fall within a well-supported Sida core clade. This clade, which also includes the genus Dendrosida, groups species with a basic chromosome number of seven. Several species are placed outside of the Sida core, confirming preliminary suggestions of the paraphyly of this group based on morphological and cytogenetic evidence. Other sections, such as sect. Nelavagae, are monophyletic and sister to the Sida core, whereas sect. Malachroideae is placed outside of the Sida core in an unresolved position. Meximalva and Sidastrum as well as an Australian group of Sida species form a well-supported clade. Sida hookeriana and S. hermaphrodita are placed in a clade and associated with Sidasodes, removed from the Sida core, indicating a position much closer to subtribe Malvineae than previously suggested. Molecular evidence does not provide clear limits to the Sida generic alliance as currently circumscribed.