Re-examination of morphological features and newly executed molecular analysis based on chloroplast (rbcL, rps4, and trnL-F) and nuclear (ITS1&2) genomes revealed unexpected diversity in Symphyodon perrottetii Mont. s. l. (Symphyodontaceae) in East and Southeast Asia. Japanese plants previously recognized as S. perrottetii are shown to include at least five different species: S. asper (Mitt.) A.Jaeger, S. copelandii Broth., S. gollanioides Nog., S. recurvomarginatus (Dixon & Sakurai) H.Akiyama, comb. nov. and S. rheophilus H.Akiyama, sp. nov. In addition, previous Japanese record of S. echinatus (Mitt.) A.Jaeger is actually S. asper. Symphyodon longispinosus H.Akiyama, sp. nov. from southwestern China is newly described. Subsequently, S. perrottetii s. str. is excluded from China and Japan and has its revised distribution range from southwest India (type locality of S. perrottetii), Sri Lanka, central Thailand, and Singapore. Symphyodon merrillii Broth., once regarded as a synonym of S. perrottetii, is again recognized as a distinct species with its distribution in Malesia and Indochina. Symphyodon ovalifolius H.Akiyama & M.Suleiman, sp. nov. is described and classified under the subgenus Parasymphyodon H.Akiyama & M.Suleiman, subg. nov. Rheoshevockia fontana Ignatov, W.Z.Ma & D.G.Long is again demonstrated to have a unique systematic position sister to the genus Symphyodon.