The taxonomic status of millipedes of the genus Spirobolus Brandt, 1833, referred to as “Yaeyama-maruyasude” from the Yaeyama Islands, Ryukyu Islands, Japan, was unresolved. We assess the taxonomic status of these Yaeyama Spirobolus sp. using an integrated morphological and molecular approach, and describe them as a new species, S. akamma sp. nov., for which partial sequences of the nuclear 28S ribosomal RNA, mitochondrial cytochrome c oxidase subunit I, and 16S ribosomal RNA markers are provided. This new species differs from continental China and Taiwan endemic congeners in anterior gonopod morphology (in having an elongate and subtriangular coxa, and a pentagonal mesal sternal process), posterior gonopod morphology (in having a coronoid prefemoral endite with rounded distal end, and an elongate telopodite), and in having four serrations on the cyphopod lateral flange.