The population of the remote Australian Northern Territory (NT) experiences a distinctive and challenging infectious disease burden. This presentation encompasses two narratives of NT-focussed work that have occupied over 30 years. Consistent with the rest of the world, C. trachomatis is a major cause of sexually transmitted infections (STIs). However, in the NT, it also causes the distinctive ocular disease trachoma, which is transmitted amongst young children in facial secretions, and is not regarded as an STI. In the 1980s and 1990s, ocular isolates were obtained from children in the remote NT, associated with clinical patterns consistent with trachoma. Whole genome analysis revealed three lineages all unrelated to ‘ocular” strains elsewhere in the world, apart from at the ompA, and pmpEFGH genes, for which “ocular” variants appear to have been acquired by recombination. Subsequent work has shown that one lineage is globally distributed, and is weakly tropic, so often also associated with STIs. There is no evidence that the other two exist outside Australia, and they have strong ocular tropism. These data have assisted the development of a C. trachomatis genotyping method, CtGEM, that identifies ocular lineages known to exist globally, and also discriminates the major phylogenetic groups of the entire species. There is a high burden of skin infections in the remote NT, and Streptococcus pyogenes is largely responsible. It is likely that this contributes to the high prevalence and incidence of rheumatic heart disease in the NT. An effective S. pyogenes vaccine would be of considerable benefit. It is unclear with emm type-specific or non-specific vaccine have the greatest potential. Analysis of emm types from 1810 isolates collected in the NT since 1987 indicates that a 30-valent emm type-specific prototype vaccine developed in the United States will have poor efficacy in the NT, unless there is cross protection between emm types, and a strategy for eliciting immunity against emm cluster D4 is developed. Possible priorities for research will be discussed.