The 12 species of Solanum sect. Micracantha are part of the large subgenus Leptostemonum or “spiny solanums,” which includes some 350–400 species. Members of the section are found in the Neotropics and are characterized by a combination of characters including a viny, climbing habit using recurved prickles, unbranched inflorescences, deeply divided corollas, and glabrous fruits. Broad-scale phylogenetic relationships within the spiny solanums have been the subject of several recent studies, but many of the individual groups, including sect. Micracantha, have received little attention. In this study we infer relationships within sect. Micracantha and its placement within the spiny solanums using DNA sequence data from three chloroplast markers, trnT-F, rpl32-trnL, and ndhF-rpl32 and five nuclear markers, ITS, waxy, and three COSII markers: At1g44760 (COS4b), At1g50020 (COS5c), and At2g15890 (COS5). Results support the monophyly of sect. Micracantha (the Micracantha clade) and its sister relationship with the Bahamense clade of the spiny solanums. Within sect. Micracantha it appears that characteristics such as fruit size and habit are more strongly correlated with the habitat in which the species grow than with the phylogeny. The COSII markers had numerous parsimony-informative characters and are similar in their utility to the more commonly used ITS and waxy markers. The trnT-F chloroplast marker resolved more nodes than the ndhF-rpl32 and the rpl32-trnL markers in parsimony analyses, despite the greater number of parsimony-informative characters in rpl32-trnL.