The first step of any metagenome sequencing project is to get the inventory ofOTU abundances (operational taxonomic units) and/or metagenomic gene abun-dances. The former is generated with 16S‐rRNA‐tagged amplicon sequencing tech-nology, and the latter can be generated from either gene‐targeted or whole‐sample shotgun metagenomics technologies. With 16S‐rRNA data sets, measuringcommunity diversity with diversity indexes such as species richness and Shannon'sindex has been a de facto standard analysis; nevertheless, similarly comprehensiveapproaches to metagenomic gene abundances are still largely missing, despite thatboth OTU and gene abundances are DNA reads. Here, we adapt the Hill numbers,which were reintroduced to macrocommunity ecology recently and are nowwidely regarded as a most appropriate measure system for ecological diversity,for measuring metagenome alpha‐, beta‐ and gamma‐diversities, and similarity. Ourproposal includes the following: (a) Metagenomic gene (MG) diversity measures thesingle‐gene‐level metagenome diversity; (b) Type‐I metagenome functional gene clus-ter (MFGC) diversity measures the diversity of functional gene clusters but ignor-ing within‐cluster gene abundance information; (c) Type‐II MFGC diversityconsiders within‐cluster gene abundances information and integrates gene‐cluster‐level metagenome diversity and functional gene redundancy information; and (d)Four classes of Hill‐numbers‐based similarity metrics, including local gene overlap,regional gene overlap, gene homogeneity measure and gene turnover complement,were introduced in terms of MG and MFGC, respectively. We demonstrate theproposal with the gut metagenomes from healthy and IBD (inflammatory boweldisease) cohorts. The Hill numbers offer a unified approach to cohesively andcomprehensively measuring the ecological and metagenome diversities ofmicrobiomes.