Biodiversity is the product of millions of years of evolution and forms the basis of earth‘s life support system, but the magnitude and relative diversity of global species richness remains unknown. On earth there may be over 100 million speciesbut fewer than 2 million have been formally described. Coverage across different biological groups is very uneven with a known taxonomic deficit especially marked for microfauna and meiofauna due to problematic identification and hyper abundant representatives. Soft-bottom benthic meiofauna are ubiquitous, highly abundant organisms that play a crucial role in marine ecosystem functioning. Nevertheless, quantifying community structure using standard morphological approaches requires highly skilled taxonomists that are in short supply, and is very time consuming. The development of massively parallel sequencing has paved the way to explore microbial and meiofaunal diversity in time and space. Several studies have used pyrosequencing to assess the diversity of bacteria and archaea in the marine environment but there has been comparatively limited focus on eukaryotes. Moreover, diversity estimates derived from earlier second-generation sequencing studies are now known to be artificially inflated and skewed, due to several problems ranging from DNA manipulation and PCR amplifications to bioinformatic analyses. Here, I initially provide an overview of the emerging field of meiofaunal biodiversity assessment, using 454 Roche sequencing. The field differs substantially from environmental sequencing of prokaryotes and even some protists and so warrants separate attention. Empirically, meiobenthic richness of numerous phyla was estimated at alpha (local) and beta (European) scales, illustrating the extensive, but also spatial nature of meiofaunal richness and putative distribution patterns.Further to this, I sequenced carefully constructed artificial nematode control communities to assess the drivers (richness and genetic diversity) of DNA recombinant (or chimera) formation in environmental DNA PCR reactions. Theseadvancesprovide a fast, objective and cost-effective wayof accuratelyexploring and elucidating biodiversity in environmental samples.