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Piscirickettsiosis, the cause of great losses in Chilean salmonid population, is produced by Piscirickettsia salmonis. The bacterium has developed resistance to treatments over time, including antibiotics and vaccines, due to a variety of evasive strategies, including biofilm formation. The bacterium has genomic islands, clusters of relevant genes that vary between genomes. This work aimed to analyze the relationship between number of pathogenic islands and their virulence genes in complete genomes from different strains of EM and LF genogroups, besides the search for genomic islands with non-virulent factors, like metabolic islands and fitness. Furthermore, we evaluated conservation and variation between strains from different genogroup, considering LF-89 (ATCC) and Psal-001 as reference strains, analyzing genomes through averages by two bioinformatic tools. About 13 pathogenic islands/strain were quantified, with 1 to 47 loci/island with unique behaviors for genogroup. Comparing islands regarding genomes, higher conservation rate was seen in EM genogroup, against oscillating values within LF genogroup strains. Non-virulent factors were also found. Overall, EM genogroup showed greater convergence in island conservation between strains concerning the pathogenic function compared to LF strains. Finally, different transposases were found to support high genomic plasticity and the scarcity of cured genes complicated correct identification.