Data on the genomics of Porphyromonas species other than Porphyromonas gingivalis (POTG), particularly within pulmonary environments, are scarce. In this study, we conducted whole genome sequencing (WGS) on pulmonary isolates of POTG, specifically P. catoniae (n=3), P. pasteri (n=1), and P. uenonis (n=2), from people with cystic fibrosis. These genomic analyses were complemented with antimicrobial susceptibility tests for these strains. We compared the genomic sequences of these pulmonary isolates with those of previously characterized Porphyromonas species. Our study revealed a distinct clade differentiation between non-pigmented and pigmented Porphyromonas species. Interestingly, unlike P. gingivalis, the pulmonary POTG strains lacked known virulence genes, except a putative hemolysin gene. Regarding antibiotic resistance, notable resistances were limited to vancomycin in P. catoniae and clindamycin in P. uenonis. These findings support the hypothesis that POTG species may predominantly behave as commensals in the lung environment rather than as pathogens.