Hydrangea marunoi Tagane & S. Fujii, from the Kimotsuki Mountains in the Ohsumi Peninsula, southern Japan, is described and illustrated. It is morphologically similar to H. alternifolia in having three-petaloid calyx lobes in marginal flowers, but is distinguished by the larger stamen number, and longer styles and seeds. Multiplex ISSR genotyping by sequencing (MIG-seq) demonstrated that the new species is monophyletic and closely related to H. amamiohsimensis and H. moellendorffii rather than H. alternifolia.