Legionella systems for secreting effector proteins into the host cell environment are a key factor in intracellular survival and virulence827. Confirming and extending a previous finding8, we identified that the Dot/Icm type IVB secretion system (T4BSS) and Lsp type II secretion system (T2SS) belonged to the core genome of all Legionella species. However, we found that Legionella species are variable in their type IVA secretion systems (T4ASS) as they were present in different species except for the P-type, which was present in all species and codes for conjugative pili required for mating828 (Table 1). The F-type T4ASS also codes for pili but was missing from genomes Lp2, Lp3, Lp6 and L. cherii while the Lvh (Legionella virB homologue) T4ASS, which is involved in spread of infection from environmental niches828, was identified in only 10 Legionella genomes: 6 genomes from Clade 1; and 2 from Clade 3 (L. bozemanii serogroup 2 and L. dumoffii) (Table 1). Interestingly, Lp3 and Lp6 had Lvh T4ASS but not the F-type T4ASS in their genomes. Recently identified Genomic Islands (GI) T4SS (GI-T4SS), GI-T4SS-1 and GI-T4SS-2, which were found in Lp 130b and recognized to be involved in host adaptation29, were identified across Lp serogroups; 2 clusters each were present in Lp6, Lp11, Lp12, and Lp16 while a single cluster was present in Lp3, Lp7 Lp10, and Lp17 (Table 1). A single cluster of GI-T4SS (GI-T4SS-1) was also identified in non-Lp species L. cherii and L. dumoffii, both in Clade 3.