Long-read sequencing is currently supported by sequencing platforms from Pacific Biosciences and Oxford Nanopore Technologies, both of which generate ultra-long reads. Metabarcoding and metagenomics are the two approaches used when implementing sequencing. Metabarcoding involves the amplification and sequencing of selected nucleic acid regions, while in a metagenomic approach extracted nucleic acids are sequenced directly without prior amplification. Both approaches have associated advantages and disadvantages, which, in combination with long-read sequencing, provide a promising new approach for fungal identification and diagnosis of mycoses, on which we will reflect in this short review.