Bacterial Gill Disease (BGD) is a condition caused by multiple bacterial species which affects salmonids and can cause large economic losses in hatcheries. This disease is characterized by bacterial overgrowth on and fusion of the gill filaments. Infected fish will “lurk” at water inlets and have a swollen or engorged appearance to their gills. The bacterial colonization eventually causes suffocation and is especially lethal for small fish and fry. BGD prevalence is linked to water quality and is often found in hatchery tanks with recirculation systems having poor water quality. There are several bacterial pathogens which are suspected to cause BGD in brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta). Die off of a tank population may occur within 24 hours of infection. BGD identification is often not feasible due to the time and cost of bacterial culturing. The goal of this research is to rapidly identify species of bacteria present on suspected infected trout using the molecular tools of Polymerase Chain Reaction (PCR) and Gel Electrophoresis. Preliminary results have identified Pseudomonas fluorescens on fish gills and tank filters. Ongoing research seeks to identify other target species (Flavobacterium branchiophila and Aeromonas salmonicida) through nested PCR targeting the 16srRNA region using universal and species specific primers. Purified PCR product will be sent for sequencing for phylogenetic and future metagenomic study.