Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae leading to benthic recolonization of disturbed areas of the seafloor. Here we use a tree-of-life (TOL) metabarcoding approach to investigate the species richness, diversity, and spatial variability of the larval assemblage at mesoscales across the abyssal seafloor in two mining-claim areas in the eastern Clarion Clipperton Fracture Zone (CCZ; abyssal Pacific). Our approach revealed a previously unknown taxonomic richness within the meroplankton assemblage, detecting larvae from 12 phyla, 23 Classes, 46 Orders, and 65 Families, including a number of taxa not previously reported at abyssal depths or within the Pacific Ocean. A novel suite of parasitic copepods and worms were sampled, from families that are known to associate with other benthic invertebrates or demersal fishes as hosts. Larval assemblages were patchily distributed at the mesoscale, with little similarity in OTUs detected among deployments even within the same 30 x 30 km study area. Our results provide baseline observations on larval diversity prior to polymetallic nodule mining in this region, and emphasize our overwhelming lack of knowledge regarding larvae of the benthic boundary layer in abyssal plain ecosystems.