The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, 'usual' (U) and 'gray' (G), of the short-spined sea urchin Strongylocentrotus intermedius. The genome sequences are 15,705 bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (D xy = 0.0083 ± 0.0007) is detected between the forms. The GenBank (KC490912) mt genome of S. intermedius is much closer to the U form (D xy = 0.0013 ± 0.0003) than to the G form (D xy = 0.0085 ± 0.0006), demonstrating unique evolutionary trajectories for each form, which we previously suggested based on the bindin gene and symbiont analyses
