Honeybees are an important pollinator around the world and is used in agriculture, the bees also make products like honey, royal jelly and wax these products make up a market worth 15 billion dollars in the US. Honeybees are on the decline and a problem might be damage to the microbiota in the gut. The MinION is a next generation sequencing tool created by nanopore technologies; it’s often compared to Illumina sequencing. MinION is believed to be relatively inaccurate compared to other sequencing tools, MinION utilizes nanopores to measure electrical signals from the different nucleotides. The aim of this study was to analyze the MinIONs accuracy in identifying bacteria, and analyzing if the MinION is a tool appropriate to use in understanding the gut microbiota of bees. Bacteria was grown on LB plates and the genetic DNA was isolated and amplified using PCR. The 16S gene was sequenced using MinION and analyzed using the Epi2me desktop agent. The large number of analyzing shows that there are about 40% of the materials that never get approved by Epi2me. When identifying bacteria the program showed to be accurate in most cases even the contaminated samples were identified with high accuracy. However, Epi2me had some difficulties correctly identifying specific closely related bacteria. In conclusion the identifying bacterial species using MinION together with the Epi2me software was concluded to be accurate in the majority of cases even though a few blind spots were experienced.