The continuous rise in global human population makes the expansion and intensification of our current food production systems necessary. Aquaponics is a solution for sustainable production of fish and plants in a semi-closed system, where nutrient-rich water from the fish provides nutrients for plant growth. Development of environmentally sustainable production of plants and fish using aquaponics requires a complete understanding of the biological components of the system. In particular, aquaponics is dependent on bacteria to mineralise fish waste. These bacterial populations in aquaponic systems are highly diverse, whether between systems or between the different compartments within a system. Description of the bacterial communities in aquaponics is of interest not only because it increases our understanding of the system's microbial ecology, but also provides a basis for managing these communities to enhance their function and reliability. This project aims to characterise microbial populations in different zones of grow-bed, fish gut, and plant roots of aquaponic systems using metagenomic DNA sequencing techniques.