Overall, the population assignment of Legionella genomes was correlated to the groupings of ML-based phylogeny (Fig. 1a), BAPS, and fineSTRUCTURE, even though there were differences in population assignments at the lowest resolution within a clade, mainly due to methodological differences in the sensitivity of each method in assigning into populations. fineSTRUCTURE grouped Lp into 9 groups. However, BAPS clustered Lp serogroups into 7 groups. The main difference was that one large cluster assigned by BAPS included Lp2, 4, 5, 7, 9 11, 14, and 16 but were split into three groups by fineSTRUCTURE. In addition, fineSTRUCTURE grouped Lp1 Paris into a single cluster whereas BAPS grouped it with Lp HL06041035 and Lp13. While BAPS grouped species in Clade 2 into 4 groups, fineSTRUCTURE grouped them into 5. The main differences were that BAPs grouped L. erythra and L. birminghamensis into two separate populations while fineSTRUCTURE assigned them to a single population. Similarly, fineSTRUCTURE assigned L. jordanis and L. nautram into 2 singleton populations but BAPS grouped them together into 2 separate populations along with 2 other Legionella species in each of the populations. Clade 3 species were grouped into 4 populations in the BAPS analysis while fineSTRUCTURE grouped them into 6 populations by splitting the BAPS populations again into finer populations as well as re-assigning species into different populations. The single Clade 4 species, L. rowbothamii, was s distinct population in BAPS analysis (Fig. 5).