AimsTo investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small-scale farms as well as homestead gardens using pyrosequencing. Methods and ResultsNext generation sequencing analysis of the V1-V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (645%), class Gammaproteobacteria (566%) and genus Aeromonas (144%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (163%) from the one commercial farm harboured more sequences than cabbage from the small-scale farm (13%) or homestead gardens (19%). Escherichia sequences were detected in both irrigation water (46%) and on cabbage (13%) samples from the small-scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (19%) from the small-scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens. ConclusionWater sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop. Significance and Impact of the StudyMicrobial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.