The plant origin of the bee products often influences their value. Here, we investigated for the first time how the content of bee bread, a functional food with high nutritional value, differs in terms of plant and bacterial taxa in comparison with bee pollen and honey samples, using shotgun sequencing analysis. Sequencing of honey, bee pollen, and bee bread samples yielded approximately 32.74 Gbp of data. Out of a total of 268,964 abundant genes, 70,280 genes (26.13%) were assigned to a taxonomic group according to the supermajority rule. These taxonomic groups were annotated as follows: Kingdom (84.99%), phylum (75.94%), class (73.26%), order (67.21%), and family (65.11%). It was determined that honey, bee pollen, and bee bread samples consisted of large plant families Poaceae, Fabaceae and Asteraceae. This indicates that these taxa are also favored by bees for visiting, and are therefore used as food sources. These differences vary according to the environmental flora of the apiary and may be site specific. Based on these results, DNA-based next-generation sequencing techniques can be successfully used to identify the plant sources of bee products. Thus, the botanical and geographical origin of bee product samples can be more accurately, reliably and in detail identified. Furthermore, this technique can be successfully used to monitor the regional flora and food safety.