Over the course of the recent decade, the composition of Alsineae has been drastically changed by means of molecular phylogeny. However, the genus Brachystemma has not been sampled in any of the previous studies, and its phylogenetic position is still pending. In addition, the related species Stellaria ovatifolia, which has at times been placed in Brachystemma, Schizotechium, or Stellaria, has also not been sampled. Here, nuclear ribosomal internal transcribed spacer (ITS) and four plastid regions (trnL-F, matK, rbcL, rps16) were used to conduct phylogenetic analyses within Caryophyllaceae and the tribe Alsineae. Ancestral characters (petal margin and number of seeds) were reconstructed in the tribe Alsineae based on the phylogenetic results. Our results indicate that Brachystemma is nested in the tribe Alsineae and forms a monophylum with S. ovatifolia, and apically lobed petals and numerous seeds may be the ancestral characters in the tribe Alsineae. Based on our study, Stellaria ovatifolia should be considered within Brachystemma, and Brachystemma is clearly a separate genus and now includes two species.