Mangrove sediments have a very high composition of meiofauna, which is prominent in the nutrient cycle of the mangrove environment. The present study is the first of its kind in the Andaman Islands on the vertical distribution of meiofauna. The meiofauna was observed vertically in the sediment of mangrove environments of three locations of South Andaman, namely Chidiyatapu, Carbyns Cove, and Burmanala. The collected sediments were divided into three strata (top 3 cm, 3–6 cm, and 6–9 cm). Nine significant groups were observed, namely Nematoda, Polychaeta, Copepoda, Foraminifera, Diatoms, Gastrotricha, Kinorhyncha, Oligochaeta, and Halacaroidea, among which Nematoda (79%) was identified as the most abundant, followed by Diatoms. The species Nematodes dominated all stations, except Burmanala at a depth of 6–9 cm. Meiofauna abundance decreased as the depth increased due to anaerobic conditions and less food availability, which followed the global trends in mangrove sediments. Most of the individuals were observed from the Carbyns Cove, and the least from the Burmanala sediments. Though less abundant, diversity and evenness of groups were high in Burmanala, while species richness was higher in Chidiyatapu and Carbyns Cove. The study results highlighted how sites affect the response of a given genus of nematode to the sedimentary environment, and it is the first of its kind in the Andaman Islands.