A quadrannulate species of Orobdella, O. kanaekoikeae sp. nov., from the mountainous region of Shikoku, Japan is described. This new species is small with a body length of mature individuals reaching only ca. 5 cm. Phylogenetic analyses using nuclear 18S, histone H3, mitochondrial cytochrome c oxidase subunit I, tRNA^Cys, tRNA^Met, 12S rRNA, tRNA^Val, 16S rRNA, tRNA^Leu, and NADH dehydrogenase subunit 1 markers showed that O. kanaekoikeae is a sister species of the quadrannulate small O. brachyepididymis. Phylogenetic relationships among populations of this new species were also estimated using mitochondrial DNA markers. Additionally, transmission electron micrographs of a capsule-like structure obtained from a post-copulatory individual revealed that the capsule contained spermatozoa, and was thus defined as the spermatophore. The gastroporal duct of Orobdella leeches is an accessory copulatory organ that receives a spermatophore during copulation.