Meiofauna communities were analysed from samples collected at four stations on the Kenyan continental shelf (Shimoni, Kwale, Mombasa and Kilifi) during the maiden cruise of the RV Mtafiti, 12–21 December 2015. Nematodes were identified to genus level, and their distribution and composition were mainly influenced by grain size distribution, a finding similar to studies in other areas with a similar grain size distribution (iso-communities). The southern stations (Shimoni and Kwale) had coarser sediments than the northern stations (Mombasa and Kilifi). The family Chromadoridae was dominant at Shimoni, while Cyatholaimidae dominated at Kwale. Mombasa was dominated by Chromadoridae, Cyatholaimidae and Oxystominidae, and Kilifi by Xyalidae. The dominant genera portrayed a trend similar to that observed in the families, in that the dominant genera were members of the dominant families. Spilophorella was dominant at Shimoni, and Paracanthonchus, Paracyatholaimus, Desmodora, Microlaimus and Draconema were dominant at Kwale and Mombasa. Microlaimus, Daptonema and Terschellingia represented the highest abundances at Kilifi. All stations were dominated by epistratum feeders. Selective deposit feeders were the second-most-dominant feeding guild at Mombasa and Kwale, whereas non-selective feeders had the second-highest abundance at Kilifi. The diversity index was highest at Mombasa and lowest at Shimoni, whereas dominance was highest at Shimoni and lowest at Mombasa.