We describe a new technique to determine the harvest location of Merlangius merlangus (whiting) based on exploiting the natural bacterial populations associated with the mucus layer of fish and surrounding seawater as biological tags. Bacterial community profiles from the outer and mouth mucus and the surrounding seawater were characterized by terminal restriction fragment length polymorphism (T-RFLP), and fish harvest location was predicted based on T-RFLP profile comparisons between fish and water and between individual fish. Fish harvest location was not resolved reliably based on analysis of the shared seawater and outer-mucus markers. However, comparisons based on shared seawater and mouth-mucus markers placed fish within 1.92 (± standard error (SE) of 0.31) stations (p < 0.002), equivalent to 153.0 km, of their known harvest location. Fish placement resolution was further increased when fish-to-fish bacterial assemblage comparisons were made. Based on outer-mucus, mouth-mucus, and combined outer- and mouth-mucus analysis, fish were placed within 1.00 (±SE 0.27), 1.55 (±SE 0.28), and 0.71 (±SE 0.24) (p < 0.04) stations, equivalent to 79.7, 123.5, and 57.3 km, respectively, of their known harvest location.