In this study a Sipuncula species Phascolosoma sp. was collected from seagrass area from Chuuk lagoon Micronesia and its complete mitochondrial genome analyzed. This is the second complete mitochondrial genome record from the genus after Phascolosoma esculenta. The total length of mitochondrial genome of the species is 16,571 bp, which is longer than P. esculenta record. Also, locations of tRNA-Gly and putative control region are different between two records. Furthermore, phylogenetic relationship of Phascolosoma sp. are investigated due to protein-coding genes of mitochondrial genome. Due to the lack of recorded data, P. esculenta has been observed is the closest species to Phascolosoma sp. and they are belonging to the monophyletic group.