To improve the accessibility of genomics for the identification of wood inhabiting microorganisms to FPInnovations’ members, we compared three different methods for metabarcoding on environmental DNA (eDNA): cloning with first generation Sanger sequencing, amplicon metabarcoding with second generation Illumina sequencing, and lastly amplicon metabarcoding with third generation, long read sequencing with the portable MinION. We looked at costs for each method, speed, and difficulty. Illumina metabarcoding was the most economically feasible method. Cloning was difficult, being prone to failure and requiring extensive trouble shooting to complete. Illumina metabarcoding must be outsourced which can take more time for project completion; however, little in-house troubleshooting is necessary. Third generation sequencing is an attractive alternative for routine analysis. It is rapid, low-cost, and takes little up-front capital for start-up. However, it may not be feasible if used infrequently given the time required to learn the technology and the rapid expiration of unused flow cells. For occasional projects, it is recommended to outsource amplicon metabarcoding to a facility that sequences either with second or third generation sequencers, including data analysis.