The vertical distribution of meiofauna within subtidal sediments was studied in four stations pertaining to mangrove or muddy flats habitats. In 2003, replicated samples were taken in dry (February) and wet (July) seasons at the Bacunagua Inlet, southwestern coast of Cuba. The abundance and number of meiofaunal taxa exhibited a vertical gradient possibly due to changes in the concentrations of oxygen and hydrogen sulphide, rather than food availability along this gradient. Nematodes are capable of distributing themselves throughout the whole sediment column due to their ability to tolerate reducing conditions; however depletion of communities along depth was evident. Their presence in deeper sediments (6 - 10 cm) suggests that certain species are adequately adapted to spend their entire life cycle in these harsh environments (where soluble tannins and decomposing organic matter predominate). Copepods showed a strong limitation to vertical distribution (concentrating in the top 2 cm), possibly in response to a sharp vertical decline in oxygenation within these organically enriched sediments.