Chlamydia trachomatis is the leading infectious cause of preventable blindness and the most common sexually transmitted bacterium worldwide. Trachoma presents an environment in which to investigate chlamydial pathogenicity, the conjunctivae serving as an accessible model with an objectively observable phenotype. The Bijagós Archipelago is a unique setting where trachoma is hyperendemic. The primary aims of this study were to use novel molecular, bioinformatic and geostatistical approaches in conjunction with population-based clinical and epidemiological metadata to investigate the micro-epidemiology of ocular C. trachomatis and active trachoma in this population. The prevalence of trachoma and ocular C. trachomatis infection have been documented, and socio-environmental risk factors have been identified that may be important in the implementation of trachoma elimination activities in these communities. A strong association was found between C. trachomatis ocular load (estimated using droplet digital PCR) and the level of conjunctival inflammation. Geostatistical analyses suggest that ocular C. trachomatis load may be important in transmission, as spatial clusters of high load infections were identified, whilst spatial clusters of low load infections were absent. This study includes the first population-based pathogen genome-wide association scan (GWAS) for C. trachomatis, using high quality next generation whole genome sequence data obtained directly from clinical samples. The genomewide associations with conjunctival inflammation (incE) and C. trachomatis load (mutY and CTA_0271) present genes involved in specific biological characteristics of C. trachomatis, the functions of which suggest that early interactions with host cells are important in C. trachomatis pathogenesis. Pathogen GWAS, applied in this context, is a powerful approach in the identification of multiple targets for further study in pathogenesis and directed study of potential vaccine candidates, allowing a greater understanding of association and interaction of genes on a genome-wide scale. Following a single round of mass drug treatment with oral azithromycin (MDA) in these communities the prevalence of active trachoma and ocular C. trachomatis were significantly reduced. Individual and median loads of C. trachomatis were reduced and the highest burden of disease and infection were concentrated in young children. Spatial clustering of infection identified using geostatistical tools was intensified following MDA, but the number of clusters of high load infections was reduced. The severity of conjunctival inflammation was reduced following MDA. This study suggests that chlamydial load is important in disease pathogenesis and may be important in transmission of infection. Geospatial tools may be useful in the context of MDA to identify clusters of infection and thresholds of C. trachomatis bacterial load that may be important foci of transmission. The association between conjunctival inflammation and C. trachomatis load may reflect pathogen virulence. This is supported by the presence of genome-wide associations with C. trachomatis load and conjunctival inflammation identified by pathogen GWAS. Further epidemiological, in vitro and in silico studies are required to provide a more complete picture of the relationship between disease severity, bacterial load and chlamydial diversity in the context of transmission and elimination dynamics.