The diagnosis of bacterial fish diseases has progressed from traditional culture-dependent methods involving the recovery of pathogens on agar-containing media and identification by examination of phenotypic traits. Newer approaches centre on culture-independent approaches. A problem with culturing is that it lacks sensitivity, tends to be slow, and its success depends on the composition of the media and incubation conditions employed. In contrast, culture-independent methods, now centring on molecular methods, are highly specific and sensitive. This raises an important issue that detection of very low numbers of bacterial cells does not necessarily imply the presence of clinical disease. Positivity could reflect background populations of the pathogen that may be present in the aquatic environment.