The annual sea ice that forms around the Antarctic continent is a harsh environment with steep gradients in temperature, light, salinity and nutrient concentrations. However, sea ice is a biologically active habitat where diverse microbial communities are able to survive. The aim of this study is to describe and understand microbial diversity in sea ice and to search for prokaryotes that utilize light energy without chlorophyll. Culture-independent techniques were employed to study the bacterial 16S rRNA gene diversity and presence of phototrophic bacteria in Antarctic sea-ice, brine and sea-water samples collected from a series of sites along the Ross Sea region. In this study, we used both genomic DNA and complementary DNA transcribed from messenger RNA (mRNA). Proteorhodopsin (PR) and actinorhodopsin (AR) genes are amongst the targeted ‘new-age’ phototrophic bacteria, which convert light energy to ATP via a proton pump. These bacterial rhodopsins are present in various Bacteria and Archaea classes and have been found in a wide variety of oceanic and, very recently, even freshwater environments. Degenerate primers were employed to amplify the gene from the Antarctic environmental samples. Sequences derived from this study were checked against published databases like NCBI and CAMERA. Besides Proteobacteria, which makes up the major group of bacteria in this 16S rRNA study, Bacteroidetes and Actinobacteria are also present. Based on this observation, our results show strong indication of rhodopsin-bearing bacteria. Additionally, we found strong evidence that these bacteria are active through the presence of mRNA encoding for the PR gene and that this alternate light-harvesting protein does contribute to the sea-ice ecosystem. Confirming the presence of this novel prokaryote gene in one of the last wilderness frontiers contributes considerably to our understanding of the ecology of Antarctic sea-ice communities. This project contributes to the Latitudinal Gradient Project, which is initiated by Antarctica-New Zealand.