Five species of gobiid fish are recognized in the fresh waters of Greece. Most distinctive is the south-western Hellenic (West Balkanian component) endemic genus Economidichthys Bianco, Bullock, Miller & Roubal, 1987, with the type-species E. pygmaeus (Holly, 1929) from Lefkas, Epirus and Lake Trichonis, and E. trichonis sp. nov., from Lake Trichonis, the latter probably the smallest freshwater European teleost at maturity (female, 18·0 mm) and maximum size (male, 30·0 mm). In tributaries of the northern Aegean basin (north-eastern Hellenic freshwater fauna), two species of the Ponto-Caspian genus Knipowitschia can be identified, the widespread Kn. caucasica (Kawrajsky in Berg, 1916) (coastal plain of Macedonia and Thrace) and the endemic Kn. ihessala (Vinciguerra, 1921) (Pinios river system, Thessaly). The larger Ponto-Caspian tubenose goby, Prolerorhinus marmoratus (Pallas, 1811), occurs in the Evros (= Maritsa) (Thrace) and Strymon (Macedonia) systems. Only the genera Economidichthys and Knipowitschia are considered in this paper, being redefined in terms of osteology and head lateral-line system, and the species described in detail, with special reference to meristic variation and squamation, and, in Economidichthys, the unique perianal organ of this genus. The relationships of Economidichthys and Kn. thessala are discussed and possible scenarios for their evolution are suggested in the light of Miocene to Recent events.