Studies on the geographic distribution of Magnetotactic bacteria (MTB) revealed their ubiquitous presence in diverse habitats on all continents. However, little is known about MTB inhabitation in the Indian coastal ecosystem. Here, we investigate the diversity of Magnetospirillum sp. from the iron mineral sediments deposit of the South Kerala sedimentary basin, India using culture-independent methods. The collected sediment samples were analysed for the presence of nitrate (zinc reduction), sulphide (cline method), Fe2+, total iron (ferrozine assay) and iron minerals (XRD analysis). Based on the geochemical measurements, the sediment possesses major factors such as nutrients, pH, temperature and chemical gradients in metabolic accessible form for MTB. The cubo-octahedral crystals of the magnetosome are also evident from the TEM micrographs of magnetically enriched sediment. CARD-FISH analysis showed the presence of Magnetospirillum in all the six samples analysed. Phylogenetic analysis based on 16S rRNA gene library showed that the clones belong to the class Alphaproteobacteria and are members of the genus Magnetospirillum. The results of the species-specific PCR study are consistent with CARD-FISH analysis and the identified uncultured Magnetospirillum were morphologically and phylogenetically similar to the isolates from diverse habitat. The identification of Magnetospirillum from Indian coast supports the hypothesis of wide geographic distribution of these bacteria. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.