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Meiofauna is a group of heterotrophic organisms smaller than macroinvertebrates but larger than microfauna and characterized by groups such as testate amoebae, ciliates, and nematodes. They are a link between bacteria and resources and macroinvertebrates. However, tropical meiofauna is poorly studied; thus, our goal was to characterize meiofaunal community composition and abundance and assess potential environmental variables controlling these community dynamics. Monthly samplings of meiofauna were conducted for eight months in Quebrada Prieta, El Yunque National Forest, Puerto Rico. Sampling was made in 12 pools, and data on discharge, sediment characteristics, and biotic variables were also collected. A total of 62 meiofaunal morphospecies were identified, with nematodes dominating the community, followed by testate amoebae. Bacterivores and detritivores taxa dominated the community. Meiofaunal abundance was negatively related to discharge and positively to the percentage of coarse sand, nitrate, and macroinvertebrate abundance. The composition of meiofauna in Quebrada Prieta is like the composition reported for temperate streams, at least in major meiofaunal groups present. However, the community in Quebrada Prieta was dominated by testate amoebae. In contrast, temperate streams are often dominated by rotifers and nematodes. Both abiotic and biotic variables are important for meiofaunal communities in the headwater streams in Puerto Rico.