Magnetotactic bacteria (MTB) are morphologically and phylogenetically diverse prokaryotes commonly able to produce magnetic nanocrystals within intracellular membrane-bound organelles (i.e., magnetosomes) and to swim along geomagnetic field lines. We studied the diversity of MTB in the samples collected from a mangrove area in the Sanya River, Hainan, South China, using microscopic and microbial phylogenetic methods. Results of microanalysis and observation in microscopy and energy dispersive X-ray spectroscopy (EDXS) reveal a highly morphological diversity of MTB including unicellular cocci, vibrios, rod-shaped bacteria, and three morphotypes of multicellular magnetotactic prokaryotes (MMPs). In addition, analysis of the 16S rRNA gene showed that these MTB were clustered into 16 operational taxonomic units affiliated to the Alpha-, Delta-, and Gamma-proteobacteria classes within the Proteobacteria phylum. Meanwhile, by using the coupled fluorescence and transmission electron microscopy analysis, rodshaped bacteria, vibrio, and cocci were phylogenetically and structurally identified at the single-cell level. This study demonstrated highly diverse MTB communities in the mangrove ecosystem and provide a new insight into the overall diversity of MTB.