Bacterial Kidney Disease (BKD) is a chronic infection of farmed salmonids caused by Renibacterium salmoninarum, a slow-growing, intracellular Gram-positive bacterium. In Chile, BKD surveillance relies primarily on ELISA and qPCR, which require fully equipped laboratories and trained personnel. Therefore, developing field-deployable diagnostic tools is a priority. Comparative whole-genome analysis of three R. salmoninarum isolates identified two unique genes, encoding an ABC-type transporter and a metabolic enzyme, without significant homology to other bacterial sequences in the NCBI database (BLAST). Specific primers for qPCR and LAMP assays were designed using Primer-BLAST and NEB LAMP Primer Design Tool v1.4.1, respectively. The LAMP assay exhibited high specificity and sensitivity comparable to qPCR, detecting DNA concentrations as low as 10⁻⁹ ng/μL. An in vivo infection trial in Salmo salar was conducted to quantify gene copy numbers at 3, 5, 15, and 30 days post-infection (dpi) in head kidney samples. LAMP consistently detected the genes in DNA throughout the infection, whereas cDNA analysis revealed variable transcriptional patterns for p57 and Metabolic, and no detectable expression for ABC. These findings suggest differential regulation of bacterial gene expression during infection, accompanied by modulation of host apoptotic genes (casp3, casp8, and casp9). The newly developed LAMP assay represents a rapid, cost-effective, and reliable diagnostic tool, suitable for on-site application and integration with host immune response profiling, offering a promising approach to enhance BKD detection and management in aquaculture.