During a study of microbial diversity in marine sponges, a mycobacterium (strain name: FSD4b-SM) was isolated in pure culture from tissue of a Fascaplysinopsis sp. sponge, taken from waters on the Great Barrier Reef in Queensland, Australia at a depth of 26 metres. FSD4b-SM replicates slowly (doubling every 15-20 days), growing preferentially in liquid sea-water media up to 30°C. Initial 16S rRNA gene sequence comparisons suggested that it was closely related to the M. tuberculosis complex (MTBC). We established the complete genome of FSD4b-SM, which consists of a single circular 5,575,519 bp chromosome harbouring 4624 protein coding DNA sequences (CDS), which makes it larger than the MTBC genomes. However, DNA and protein sequence comparisons of 2500 core CDS confirmed this mycobacterium is the most closely related species yet discovered to the tubercle bacilli. Despite the unusual origin of the bacterium, the FSD4b-SM genome revealed extensive conservation of genes associated with M. tuberculosis pathogenesis, including ESX-1, ESX-3, ESX-5 secretion system and associated effectors, PE/PPE proteins, and signature MTBC cell wall glycolipids (e.g. PGLs, mycoketides). There were 418 CDS specific to FSD4b-SM with predicted functions likely related to growth within the marine environment, including membrane antiporters and permeases, production of osmoprotectants and novel secondary metabolite loci. A further 900 CDS were present only in the MTBC. The discovery of FSD4b-SM (proposed name Mycobacterium spongiae sp. nov.) adds to growing evidence that the recent evolutionary origins of the MTBC were likely marine and provides an additional important resource as we refine our understanding of the genetic factors that shaped the evolution of M. tuberculosis.