Sequence-based typing (SBT) ofLegionella pneumophilais a valuable tool in epidemiological studies and outbreak investigations of Legionnaires’ disease. In theL. pneumophilaSBT scheme,mompS2is one of seven genes that determine the sequence type (ST). TheLegionellagenome typically contains two copies ofmompS (mompS1andmompS2).When they are non-identical it can be challenging to determine themompS2allele, and subsequently the ST, from Illumina short-reads. In our collection of 233L. pneumophilagenomes, there were 62 STs, 18 of which carried non-identicalmompScopies. Using short-reads, themompS2allele was misassembled or untypeable in several STs. Genomes belonging to ST154 and ST574, which carriedmompS1allele 7 andmompS2allele 15, were assigned an incorrectmompS2allele and/ormompSgene copy number when short-read assembled. For other isolates, mainly those carrying non-identicalmompScopies, short-read assemblers occasionally failed to resolve the structure of themompS-region, also resulting in untypeability from the short-read data. In this study, we wanted to understand the challenges we observed with calling themompS2 allele from short-reads, assess if other short-read methods were able to resolve themompS-region, and investigate the possibility of using long-reads to obtain themompSalleles, and thereby performL. pneumophilaSBT from long-reads only. We found that the choice of short-read assembler had a major impact on resolving themompS-region and thus SBT from short-reads, but no method consistently solved themompS2allele. By using Oxford Nanopore Technology (ONT) sequencing together with Trycycler and Medaka for long-read assembly and polishing we were able to resolve themompScopies and correctly identify themompS2allele, in accordance with Sanger sequencing/EQA results for all tested isolates (n=35). The remaining six genes of the SBT profile could also be determined from the ONT-only reads. The STs called from ONT-only assemblies were also consistent with hybrid-assemblies of Illumina and ONT reads. We therefore propose ONT sequencing as an alternative method to performL. pneumophilaSBT to overcome themompSchallenge observed with short-reads. To facilitate this, we have developed ONTmompS (https://github.com/marithetland/ONTmompS), anin silicoapproach to determineL. pneumophilaST from long-read or hybrid assemblies.