Antarctic ecosystems (such as the ponds by Bratina Island, Antarctica) provide an excellent opportunity to examine organisms that can live in one of the most extreme and geochemically varied environments in the world. These ponds are of interest as each one can vary greatly in size, depth, and age as well as profiles of dissolved oxygen, metal concentrations, pH and salinity. Even within ponds geochemically distinct stratified layers can form which can greatly influence their microbial communities. There are a number of studies which indicate that microbial populations found in Antarctic ponds will be highly diverse and variable due to the uniqueness of the environment. This study aims to increase our knowledge of microbial biodiversity and the environmental factors which structure them, in particular the stratification transition zones within ponds water columns. A thorough set of biological samples were taken from five selected ponds during mid-summer in the 09-10 season to complement those taken during the winter freeze-up in the 07-08 extended season by Hawes and co-workers. Oxygen concentration, pH, conductivity and temperature of each pond water sample were measured in the field and water samples were taken back to the University of Waikato for further analysis. This research primarily used the DNA fingerprinting technique ARISA, matched with geochemistry to identify and characterise the resident and functional members of the microbial community and understand how the community is structured in relation to environmental conditions. We found that the planktonic populations of the Bratina Island ponds do vary between ponds, that each pond has its own chemical signature and that populations do change with depth. One of the studied ponds, Egg, was found to have an extreme chemical stratification leading to significantly different populations at each depth. Data analysis using BEST analysis determined that the changes in the bacterial populations in Egg are primarily in relation to the pH and conductivity at each depth which changes dramatically in the lower depths.