This study performs an analytical comparative taxonomic analysis of marine gobies (the family Gobiidae) scattered along the Aegean and the Mediterranean shores of Turkey. Research study outlines the biodiversity, define regional distribution patterns, and identify ecological trends in these sensitive sea areas. Being one of the most diverse and ecologically important fish groups in shallow offshore settings, the Gobiidae family also contributes a great deal to the monitoring of habitat conditions, biogeographical dynamics as well as environmental shifts. Data collection was done across several coastal locations using consistent sampling intensities based on hand nets, visual underwater surveys, and benthic trawling. Species identification involved traditional morphological keys but natural DNA barcoding was used for distinguishing cryptic or confounding species when necessary. The two study sites recorded 45 gobiid species, demonstrating extreme differences in terms of species composition, populations, and habitat needs. Species richness along the Aegean coast exhibited increased endemism and habitat selectivity based on temperate condition and complex geological structures, and reduced sea salinity. On the contrary, high numbers of Lessepsian migrant and thermophilic species were observed in the Mediterranean coast predominantly. The research indicates that the gobiid biodiversity is heavily influenced by regional oceanographic patterns, climatic changes and human activity, such as habitat disturbance and maritime traffic. The conclusions provide reasons why taxonomic research should become an integral part of coastal management and conservation and should especially focus on early discovery of invasive species and the conservation of habitat-specific endemic gobies. The combined conclusions give us enhanced understanding of gobiid biogeography, and contribute to responsible management of Turkey’s coastal marine ecosystems.