HMP16SData provides a total of 7,641 taxonomic profiles from 16S variable regions 1–3 and 3–5 for 239 participants in the HMP whose microbiome profiles could be mapped to participant data (see the “data-raw” package directory for download and merging code), for 18 body subsites and up to 3 visits. The two variable regions, V13 and V35, identified 43,140 and 45,383 taxonomic clades, respectively, with resolution down to the genus level at a median sequencing depth of 4,428 reads per specimen. These profiles are provided as two Bioconductor SummarizedExperiment class objects: V13 and V35 (Table 1), which integrate operational taxonomic unit count data, taxonomy, a phylogenetic tree, and public-use participant information. Each object includes both 16S and MGX sample identifiers, enabling mapping and comparison with MGX profiles distributed by our curatedMetagenomicData R/Bioconductor package (7). Such a comparison is illustrated in the phylum-level relative abundance plots of matched 16S and MGX sequencing samples in Web Figure 1 (available at https://dbpia.nl.go.kr/aje). Code to reproduce Table 1 and Web Figure 1 are provided in the HMP16SData package vignette documentation along with additional analysis examples, and the color palette used in Web Figure 1 is optimized for color-blind individuals as proposed by Wong (12).