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Free-living nematodes constitute an important component of estuarine and marine benthic ecosystems. Some marine and soil nematodes are known to harbor microbes, including symbiotic bacteria and fungi, in their external cuticle as well as internally. While assessing diversity of marine nematodes from southwest England using molecular approaches, we found evidence of co-amplification of fungal 18S rRNA sequences in conjunction with nematode 18S rRNA sequences. Based on an 18S rRNA PCR-DGGE approach, 3 fungal clone types were detected alongside nematodes from 2 of 4 estuarine and marine sites in southwest England. At the phylogeny level, fungal clone type 1 belongs to Chaetothyriales while the other 2 clone types belong to Hypocreales. The fungal clones were co-amplified with specific marine nematode taxa indicating true ecological association rather than transient environmental contamination. The present study is the first to detect fungal 18S sequences in parallel with marine nematodes and opens up a new avenue of research for investigating ecological interactions between nematodes and fungi in the marine environment

Detection of fungal 18S rRNA sequences in conjunction with marine nematode 18S rRNA amplicons