Mycobacterium tuberculosis, the causative agent of the infectious disease tuberculosis, has a distinct lipid-rich cell wall. Several anti-TB drugs target cell wall biosynthetic pathways. A good understanding of its biosynthesis will provide helpful clues for the development of novel drug targets. A strategy based on random transposon (Tn) mutagenesis with two different screening criteria, altered colony morphology and mycobacteriophage resistance, was developed. Non-pathogenic Mycobacterium smegmatis and the fish pathogen Mycobacterium marinum were used for generating Tn-mutant libraries. From the colony morphology screen, two out of eight genes identified from M. smegmatis Tn-mutants and eleven out of twenty from M. marinum Tn-mutants with altered colony morphology were directly involved in cell wall synthesis. One mutant from each species was chosen for further study, the M. smegmatis 3D9 Tn-mutant with the only isocitrate dehydrogenase (icd) gene disrupted and the M. marinum 8G10 mutant with a Tn inserted into the promoter region of MMAR0978 with a deficiency in methoxymycolates production. Four mutants resistant to generalised transducing phage I3 were identified with a Tn insertion in a gene cluster involved in the biosynthesis of the cell wall associated glycopeptidolipids (GPLs), demonstrating the potential of using phage-resistant mutants for identifying cell wall biosynthetic genes.