Dataset of the complete mitogenomes of ().

is a genus of colonial stony corals that are widely distributed in the Indian and Pacific Oceans. According to the differences of microbasic p-mastigophore (MpM) nematocysts and mitochondrial haplotype, four types (type S, type H, type M and type +) were identified in this genus. There is significant genetic differentiation among those types and they belong to distinct branches in the Maximum likelihood tree, therefore they conform to the primary species hypotheses (PSHs) and the whole might be a species complex. Here we present the assembly and annotation of eleven mitogenomes of the four types and used the dataset to explore their phylogeny. The eleven mitogenomes all contained the same 13 PCGs (protein-coding genes) and two rRNA genes as the published mitogenome of (GenBank No NC_029696). However, the length of mitogenomes of distinct types varies because there are two characteristic indels in the mitogenomes, one is located at the intergenic region (IGR) of - and the other is located at the IGR of -. The phylogenetic analysis based on 13 PCGs showed that type S/M, type H and type + clustered into three separate clades. These mitogenomes will be valuable for better understanding the phylogeny, speciation, and differentiation of the species complex.