AbstractStructural variants (SVs) are variants with sizes bigger than 50 bp and capable of changing the size, copy number, location, orientation, and sequence content of genomic DNA. Although these variants have been proven to be extensive and involved in many evolutionary processes along the tree of life, there is still insufficient information on many fungal plant pathogens. In this study, the extent of SVs, as well as single-nucleotide polymorphisms (SNPs), has been determined for two prominent species of theMoniliniagenus (the causal agents of brown rot disease in pome and stone fruits):Monilinia fructicolaandMonilinia laxafor the first time. The genomes ofM. fructicolawere found to be more variant-rich in contrast toM. laxabased on the reference-based variant calling (with a total number of 266.618 and 190.599 SNPs and 1,540 and 918 SVs, respectively). The extent, as well as distribution of SVs, presented high conservation within the species and high diversity between the species. Investigation of potential functional effects of characterized variants revealed high potential relevance of SVs. Moreover, the detailed characterization of copy number variations (CNVs) for each isolate revealed that around 0.67% ofM. fructicolagenomes and 2.06% ofM. laxagenomes are copy number variables. The variant catalog as well as distinct variant dynamics within and between the species presented in this study opens doors for many further research questions.