Obtaining genome‐wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimize false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity, and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod–plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.

Among the most widely used information underpinning conservation is the concept of Red-Listing species according to criteria developed by the IUCN. The Red List designates species extinction risk based on geographic range, population size, or declines in either. However, it has frequently been questioned whether Red List criteria are appropriate for terrestrial arthropods, which comprise the bulk of animal diversity. Due to their small size, difficulty in identification, and inherent rarity, many invertebrates are hard to study, making Red List criteria hard to apply. We assess this criticism using empirical evidence from one of the largest terrestrial arthropod surveys to date, documenting the abundance and distribution of over 13,000 species in Sweden. Of these taxa, 13% have been found at a single site, and 11% of species are found only in a single weekly sample. Using these data we demonstrate that estimates of trends based on low sample sizes are associated with major uncertainty and a major risk of misclassification under IUCN criteria. We argue that even the most ambitious monitoring efforts are unlikely to produce enough observations to reliably estimate population sizes and ranges for more than a fraction of species. Thus, there is likely to be substantial uncertainty in classifying most species according to current criteria. In response, we discuss the adaptation of IUCN criteria to more accurately capture the conservation needs of invertebrates, and to adequately assess the future of the majority of global animal diversity.