Freshwater fishes in the Balkans display high percentages of endemic species, many being limited to restricted distributions. Their management, for example, through identification of priority areas for conservation or through re-introduction, is hampered by a poor understanding of their taxonomic diversity and interrelationships. We evaluate the identity of a sand goby belonging to Knipowitschia, limited to a single wetland on the Greek island of Zakynthos. Its representatives morphologically differ sufficiently from their congeners to qualify as a separate species. However, in view of the similarity in mitochondrial ribosomal DNA sequences, the evolutionary plasticity of said morphological characters, and in the absence of a taxonomic revision of the Ionian Ecoregion's Knipowitschia gobies, describing it as a new species seems unjustified and premature. Rather, we advocate that its unique habitus and its vulnerability as the island's only resident freshwater fish necessitate conservation efforts as a kind of "phenotypically significant unit". We also propose sand gobies as flagships for wetlands in the region. This case study suggests a possible approach for fish conservation prioritization in the region, taking a precautionary angle in order to avoid taxonomic inflation, which is an imminent risk given the importance of nominal species and endemics in conservation policy.