As the honey-bee gastrointestinal tract microflora and pollen are the primary sources for the honey microbial community, the aim of this work was to study and characterize the microbial transit among them. Therefore, an exhaustive microbial analysis of honey, adult honey-bee gastrointestinal tract, and pollen from different Slovakian regions and different seasons, was conducted. Microbial screening revealed that the primary sources of microbial community present in Slovakian honey are pollen and the honey-bees' digestive tract microflora, containing microorganisms normally present in dust, air and flowers. We found that the digestive tract of Slovakian adult honey-bees is highly populated by anaerobic, rather than aerobic bacteria, where coliforms, enterococci, staphylococci, Bacillus sp., Pseudomonas sp., microscopic fungi and yeast were found. Interestingly, statistical differences were found between the microflora of the gastrointestinal tract of summer and winter bees. Pollen revealed the presence of mesophil anaerobic and aerobic microorganisms, coliforms and microscopic fungi. Among these, the most representative genera were Alternaria, Cladosporium and Penicillium . In honey the counts of total anaerobic and total aerobic bacteria, that of coliforms, enterococci, bacilli, microscopic fungi and yeasts were monitored. Most frequently microscopic fungi belonging to genera Penicillium, Cladosporium and Alternaria were found.