To investigate the evolution of the batrachochytrids Batrachochytrium salamandrivorans (Bsal) and Batrachochytrium dendrobatidis (Bd) that are responsible for amphibian declines and extinctions, a new genome assembly was assembled. Prior to 2022, only a highly fragmented short-read assembly of Bsal’s genome assembly had been generated and made available, largely owing to its repeat-richness. In 2022, a new assembly based on deep nanopore long-read sequencing provided a much-needed improvement in both contiguity and completeness. Here, the road map to assembling and polishing a highly repeat-rich chytrid fungus genome using both long and short reads is described, detailing the methodology for each step, and explaining the rationales underpinning those steps. Considerations for tailoring this methodology to other similar genome assemblies are illustrated.