Diversity is a marker of ecosystem health in ecology, microbiology and immunology, with implications for disease diagnosis and infection resistance. However, accurately comparing diversity across environmental gradients is challenging, especially when number of different taxonomic groups in the community is large. Furthermore, existing approaches to estimating diversity do not perform well when the taxonomic groups in the community interact via an ecological network, such as by competing within their niche, or with mutualistic relationships. To address this, we propose DivNet, a method for estimating within-and between-community diversity in ecosystems where taxa interact via an ecological network. In particular, accounting for network structure permits more accurate estimates of alphaand beta-diversity, even in settings with a large number of taxa and a small number of samples. DivNet is fast, accurate, precise, performs well with large numbers of taxa, and is robust to both weakly and strongly networked communities. We show that the advantages of incorporating taxon interactions into diversity estimation are especially clear in analyzing microbiomes and other high-diversity, strongly networked ecosystems. Therefore, to illustrate the method, we analyze the microbiome of seafloor basalts based on a 16S amplicon sequencing dataset with 1490 taxa and 13 samples.