Still one of the most important animals on the planet, Honeybees are responsible for pollinating several species of plants that are vital to the ecosystem. They also produce honey, which is one of the few natural edible products of animal origin and has many beneficial properties for humans. Using 16S barcoding (SQK-16S024, Oxford Nanopore Technology) together with third generation sequencing MinION Mk1B and Flongle Flow Cell (Oxford Nanopore Technology) it was possible to acquire thousands of reads across the samples. The reads generated by the sequencer were analyzed using the Epi2Me software (Oxford Nanopore Technology) that identifies each sequence to species level. The initial results showed that the samples contained very small amounts of bacterial DNA. To increase the number of reads generated on each sample the number of cycles during PCR was increased. By Principal component analysis of the most common bacteria present across the samples, it was seen that in the microbiota of Swedish raw honey and processed honey there was no significant difference between them. When the Italian sample was considered in the analysis it was possible to see a significant difference between Swedish honey and Italian honey. The results suggest that different processes involved in preparing the honey to sell can cause differences in the microbiome of honey.