The aim of the study was to assess microbial microbiome of 30 honey samples and compare potential differences between the samples from apiaries and commercial trade in Slovakia and foreign countries (Latvia, Switzerland, India, Japan and Tanzania) as well as to indicate their physico-chemical and basic microbiological quality. Study of each sample consisted of physico-chemical analysis (water content, pH, free acidity and electrical conductivity), basic microbiological analysis performed by dilution plating method (total plate count, sporulating aerobic microorganisms, bacteria from Enterobacteriaceae family, preliminary lactic acid bacteria and microscopic fungi) and metagenomic analysis for bacterial diversity evaluation. Seven samples did not meet with legislative limits of physico-chemical parameters. Average values of cultivable microbial groups ranged at level 1-2 log CFU.g-1, while bacteria from Enterobacteriaceae family were not detected in any samples. Sporulating microorganisms occurred most often, in 77% of samples and yeasts were proven in 60% of samples. Bacterial diversity, determined by metagenomic analysis, was varied. We distinguished 2 groups – group A and group B. Group A contained mainly fresh (produced in 2018) Slovak and Swiss honey and we found mainly genus Lactobacillus followed by genus Bombella in them. Group B contained mainly older Slovak honey (produced in 2017) and commercial foreign samples, in which production year is difficult to know. Group B samples were interesting because of human bacteria presence with genus Prevotella dominance. Redundancy analysis showed significant connection of the electric conductivity and microbial assemblage, that indicates important influence of botanical origin to microbial representation in honey.