Bacterial disease is one of the leading causes of significant economic losses in farmed salmonid aquaculture worldwide. Early detection of bacterial disease can hasten intervention, minimizing farmed salmonid losses. The occurrence of bacterial infection in farmed salmonids has necessitated the use of antimicrobials, which is associated with the risk of antimicrobial resistance. There is a dearth of comprehensive studies on antimicrobial resistance in salmonid aquaculture, especially in Atlantic Canada. This thesis conducted a descriptive study on the frequency of bacterial isolates and antimicrobial resistance profiles of salmonid samples submitted to the Atlantic Veterinary College, Aquatic Diagnostic Services Bacteriology Laboratory (AVC ADSBL) from 2000 to 2021, which is documented in chapter 2. The most prevalent pathogens detected in the cases of samples submitted within the study period were Yersinia ruckeri type 1 (5.54%, n = 127), Renibacterium salmoninarum (2.10%, n = 48), Aeromonas salmonicida (atypical) (1.66%, n = 38), and Pseudomonas fluorescens (1.22%, n = 28). Most bacterial isolates tested for antimicrobial susceptibility (n = 918) showed resistance to florfenicol, oxytetracycline, ormetoprimsulfadimethoxine, trimethoprim-sulfamethoxazole, ampicillin, but not enrofloxacin. This thesis also developed and validated a novel main spectral profile (MSP) to identify Y. ruckeri rapidly and accurately from Atlantic salmon (Salmo salar) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (chapter 3). The analytical sensitivity of MALDI-TOF MS using the developed MSP to identify a validation set comprised of 29 Y. ruckeri isolates was 86.2%. This thesis provided valuable information on temporal trends of commonly cultured salmonid pathogens in Atlantic Canada and described their antimicrobial susceptibility profiles. These findings may influence fish veterinarians in antimicrobial selection to treat bacterial diseases of salmonids. In addition, the developed MSP has supplemented the MSPs of other Y. ruckeri in the MALDI-TOF MS reference library to facilitate the early detection of Y. ruckeri from Atlantic salmon samples submitted for bacteriology. The developed MSP can be shared with many aquatic laboratories around the world.