The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. They have been the subject of very few microbiological investigations. In particular, their microbial diversity has never been analyzed with high-throughput sequencing methods and no sequencing studies of the genomes of the microbial communities have been performed. In this article we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four different hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new taxa. Bacterial and archaeal MAGs were studied in details and showed affiliations to new species, genera, families and orders. Metabolic predictions from MAGs suggest the presence of heterotrophs and primary producers involved in the sulfur cycle. This paper, which focuses on only four of the dozens of hot springs in the Kerguelen Islands, is a preliminary study of the microorganisms, particularly thermophiles, inhabiting the hot springs of these insulated islands. These results show that more efforts should be made to better understand these ecosystems as they represent a reservoir of unknown microbial lineages and potential new metabolic pathways.