Aim. To study the blood microbiome taxonomy in patients with metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUHO).Materials and methods. The study included healthy donors without obesity (n = 116) and obese patients who were divided into subgroups with MHO (n = 36) and MUHO (n = 53). Bacterial DNA isolated from blood samples was subject to metagenomic sequencing of the v3–v4 variable region in the 16S rRNA gene. We compared the frequency of isolating certain taxa from the samples and the proportion of these taxa in the total pool of bacterial DNA in the blood.Results. MUHO patients showed an increase in Lachnospiraceae, Ruminococcaceae, and Prevotellaceae, which are the main taxa in gut microbiota. This may indicate greater intestinal permeability in such patients. Obese patients, regardless of the metabolic phenotype of obesity, more often had Rhodobacteraceae, Streptomycetaceae, Leuconostocaceae, and Burkholderiaceae DNA in their blood. Nocardioidaceae, Flavobacteriaceae, Hyphomicrobiaceae, and Gaiellaceae DNA were more frequently present in the blood microbiome of patients with MHO, whereas MUHO patients more often had S24-7, Nocardiaceae, and Helicobacteraceae DNA in their blood. Many members of these families inhabit soil and water, which may indicate increased skin barrier permeability in obese patients. Additionally, a higher number of Helicobacteraceae-positive blood samples in the MUHO patient group may indicate increased translocation from the stomach.Conclusion. Obesity is accompanied by changes in the taxonomic composition of the blood microbiome. Moreover, the nature of the changes depends on the metabolic phenotype of obesity and the permeability of external barriers.