Abstract Background Mycobacterium abscessusis an extensively drug resistant pathogen that causes pulmonary disease particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission ofM. abscessusis critically important in directing infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However there is still conflicting evidence as to howM. abscessusis acquired and whether cross-transmission occurs. Recently labs have applied whole-genome sequencing (WGS) to investigate this further and in this study we investigate whether WGS can reliably identify cross-transmission inM. abscessus. Methods We retrospectively sequenced the whole genomes of 145M. abscessusisolates from 62 patients seen at four hospitals in two countries over 16 years. Results We have shown that a comparison of a fixed number of core single nucleotide variants (SNVs) alone cannot be used to infer cross-transmission inM. abscessusbut does provide enough information to replace multiple existing molecular assays. We detected one episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired uniqueM. abscessusstrains even after spending considerable time on the same wards with otherM. abscessuspositive patients. Conclusions This novel analysis has demonstrated that the majority of patients in this study have not acquiredM. abscessusthrough direct patient-patient transmission or a common reservoir. Tracking transmission using WGS will only realise its full potential with proper environmental screening as well as patient sampling. Key points Whole genome sequencing should replace current molecular typing used routinely in clinical microbiology laboratories. Patient-to-patient spread ofM. abscessusis not common. Environmental screening may provide a better understanding acquisition ofM. abscessusinfections.