Compared with single gene analysis, multi-locus sequence data usually perform better in resolving phylogenetic relationships of closely related species. Sonneratia (Lythraceae s.l.), a genus of mangroves, is widely distributed in the Indo-West Pacific region. Sonneratia griffithii Kurz is one of the rarest species of this genus and morphological analyses have produced conflicting results regarding its affinity to other species of Sonneratia. In this study, we aimed to resolve the phylogenetic position of S. griffithii by using sequence data of the nuclear ribosomal internal transcribed spacer (nrITS) and 13 nuclear genes. We first reconstructed the phylogeny of five Sonneratia species using nrITS and the nuclear gene rpl9, which showed that S. caseolaris (L.) Engl. diverged first from the other species and that S. griffithii was closer to S. apetala Buch.-Ham. and S. ovata Backer; however, the relationships among S. griffithii, S. apetala, and S. ovata could not be resolved. Further phylogenetic analysis based on sequences of nrITS and 13 nuclear genes and using S. caseolaris as an outgroup showed that S. griffithii and S. apetala were sister species with high bootstrap support. We conclude that S. griffithii and S. apetala have the closest relationships. Furthermore, our phylogenetic analyses do not support previous intrageneric classifications of Sonneratia.