The Fynbos biome of South Africa is renowned for its high levels of plant diversity, endemism, and heterogeneous soils. Studies have elucidated the broad taxonomic classification and diversity patterns of soil nematodes in Fynbos. However, the majority of these studies have only looked at the diversity of plant-feeding nematode, and none have compared the community of free-living nematodes from different Fynbos types. We used a novel metagenetic approach to investigate variation in nematode community structure in the Fynbos vegetation. We compared 23 samples of soil nematode communities from five different Fynbos vegetation types. Nematode DNA was 454-pyrosequenced for the 18S rRNA gene. Here we show that soils from Fynbos sites (Alluvial, Sand, Limestone, Shale, and Sandstone) have distinct properties and how these influence the nematode community structure and diversity. Previous studies of free-living nematodes revealed great diversity and differentiation of nematode community structure along an environmental gradient. We found that the diversity (Shannon and Simpson index) was overall significant, but there was no difference between sites and there was no environmental gradient that seemed to delimit this diversity. Similarly, the relative abundance of dominant nematode families did not vary across sites, with the exception of Tylenchidae. The relative abundance of feeding guilds also did not vary across sites; interestingly, only plant feeding nematodes significantly varied and were negatively correlated with NH4. Furthermore, the nematode community based on Bray-Curtis distance did not cluster by Fynbos vegetation type and was significantly influenced by potassium (K) and sulphate (SO4). However, the phylogenetic signal detected that closely related taxa in Fynbos tend to co-occur more often than expected by chance. Unifrac analyses also did not cluster by vegetation type but was influenced by geographical distance. It seems that in the Fynbos there has been very little phylogenetic divergence (ecological and genetic drift) of nematode lineages. Furthermore, at a local scale the ses.NTI (nearest taxon index) was significantly higher than null expectations, indicating that co-occurrence of related nematode lineages is determined by the differences in environmental conditions across the sites. We hypothesise that in the Fynbos there is niche overlap between closely related nematodes, and nematode speciation tends to occur conservatively into closely related niches. We further propose that the phylogenetic community structure at the local scale is assembled by deterministic (rather than neutral) processes.