Croton flavens shares a general morphology with multiple species throughout Croton section Adenophylli, which has complicated the application of names to these taxa. We generated nuclear (ITS) and chloroplast (trnL-F) phylogenies of C. sect. Adenophylli in order to identify the phylogenetic placement of C. flavens and morphologically similar species. Based on these phylogenies, we recognize six subsections within the section, two of which (C. subsects. Adenophylli and Velamea) required new combinations, three others (C. subsects. Caribaeus, Laceratoglandulosus, and Meridionalis) are newly described, and one (C. subsect. Pungentes) was previously described. Croton flavens is restricted to the islands of the West Indies, extending from the Bahamas to Trinidad, but absent from the Leeward Antilles. It appears to be rare at the extremes of its range in the Bahamas and Trinidad, but otherwise it is often a ubiquitous member of dry, shrubby vegetation of many Caribbean islands. Within C. flavens we recognize a widespread typical variety and C. flavens var. pallidus from Hispaniola and Cuba.