A uniquely colored dwarfgoby, Eviota erdmanni n. sp., with a cup-like urogenital papilla in males, a cephalic sensory-canal pore system lacking only the IT pore (pattern 2), some branched pectoral-fin rays, and a dorsal/anal fin-ray formula of 9/8 is described from south Flores, Indonesia. We use molecular data from both mitochondrial and nuclear genes to infer the phylogenetic relationship of the new species with respect to its congeners, with specific emphasis on species with uniquely shaped urogenital papillae.