Mycobacterium abscessus complex is a group of rapidly growing mycobacteria, and an emerging cause of non-tuberculous mycobacterial lung disease in patients with cystic fibrosis and chronic lung diseases, such as bronchiectasis. M. abscessus complex is the most drug-resistant of the mycobacterial pathogens, resulting in limited therapeutic options and a high treatment failure rate. M. abscessus complex is comprised of three closely related subspecies: M. abscessus (sensu stricto), M. massiliense and M. bolletii. M. abscessus encodes a functional erythromycin ribosomal methylase gene, erm(41), which modifies the binding site for macrolide antibiotics, causing inducible macrolide resistance. However, this inducible macrolide resistance is not seen in M. massiliense, as the erm(41) gene of this subspecies is non-functional. Accordingly, treatment success rates with macrolide-based antibiotic treatment are much higher in patients with M. massiliense infections than in those infected with M. abscessus. Precise speciation of M. abscessus complex is important for predicting antibiotic susceptibilities and patient outcome.