Wetlands are characterised by soils rich in organic matter that accumulate carbon, providing an important pathway for carbon dioxide sequestration. Nevertheless, not all the carbon fixed can be accumulated, and a proportion will decompose through microbial consumption and be partly released into the atmosphere. Rates of organic matter decomposition in tropical wetlands and the factors associated with this process are scarce. We conducted a 2-year field study in three Melaleuca wetlands in tropical and subtropical Australia using standardised tea litter substrates (green-labile and rooibos-recalcitrant) to measure organic matter decomposition and the microbial communities associated with this process. Decomposition rates were 4-fold higher in labile litter, which was low in carbon: nitrogen, compared to recalcitrant litter. The prokaryotic communities associated with the decomposing litter were unique at each site and different from the soil. They contained taxonomic groups adapted to anaerobic, high temperatures, acidic conditions and suggestive of slow anaerobic turnover. Microbial communities changed as decomposition progressed, with the latter characterised by taxa with cellulose-degrading functions. The decomposition of recalcitrant organic matter within Melaleuca soils was relatively slow, with half of the organic matter inputs remaining after two years, supporting long-term carbon sequestration.