The Indo-West Pacific genus Hapalogenys is reviewed and two new species are described: Hapalogenys dampieriensis sp. nov. from Australia and H. filamentosus sp. nov. from the Philippines. The genus now includes: Hapalogenys analis Richardson, H. dampieriensis sp. nov., H. filamentosus sp. nov., H. kishinouyei Smith and Pope, H. merguiensis Iwatsuki, Ukkrit and Amaoka, H. nigripinnis (Schlegel in Temminck and Schlegel) and H. sennin Iwatsuki and Nakabo. Hapalogenys dampieriensis, H. filamentosus and H. kishinouyei are similar to each other in overall body appearance and are accordingly identified as the “Hapalogenys kishinouyei complex”, defined by having 2–5 longitudinal stripes on the body. Hapalogenys dampieriensis has long been confused with H. kishinouyei in having similar longitudinal dark stripes, but the two species are easily separable on meristic and morphometric values, and body colour changes with growth. Hapalogenys filamentosus differs from H. dampieriensis in having a longer pelvic fin, with the filamentous first fin ray almost reaching to or slightly beyond the base of first anal-fin spine when depressed (vs. slightly beyond anus but not reaching to base of first anal-fin spine) and two faint narrow longitudinal stripes on the body (vs. four narrow longitudinal stripes in juveniles, reducing to two with growth). A neotype is designated for H. analis. Species of Hapalogenys can be distinguished from one another on the basis of meristic and morphometric characters, body colour pattern, maximum size and distribution. The familial position of Hapalogenys is briefly discussed.