Mitochondrial genomes can be assembled readily from shotgun-sequenced DNAmixtures of mass-trapped arthropods (“mitochondrial metagenomics”), speeding upthe taxonomic characterization. Bulk sequencing was conducted on some 800 indi-viduals of Diptera obtained by canopy fogging of a single tree in Borneo dominatedby small (<1.5 mm) individuals. Specimens were split into five body size classes forDNA extraction, to equalize read numbers across specimens and to study how bodysize, a key ecological trait, interacts with species and phylogenetic diversity. Gen-ome assembly produced 304 orthologous mitochondrial contigs presumed to eachrepresent a different species. The small-bodied fraction was the by far most spe-cies-rich (187 contigs). Identification of contigs was through phylogenetic analysistogether with 56 reference mitogenomes, which placed most of the Bornean com-munity into seven clades of small-bodied species, indicating phylogenetic conserva-tion of body size. Mapping of shotgun reads against the mitogenomes showed wideranges of read abundances within each size class. Ranked read abundance plotswere largely log-linear, indicating a uniformly filled abundance spectrum, especiallyfor small-bodied species. Small-bodied species differed greatly from other sizeclasses in neutral metacommunity parameters, exhibiting greater levels of immigra-tion, besides greater total community size. We suggest that the established uses ofmitochondrial metagenomics for analysis of species and phylogenetic diversity canbe extended to parameterize recent theories of community ecology and biodiversity,and by focusing on the number mitochondria, rather than individuals, a new theo-retical framework for analysis of mitochondrial abundance spectra can be developedthat incorporates metabolic activity approximated by the count of mitochondria.