Moniliophthora perniciosa, the causal agent of wicthes´ broom disease of cacao, is one of the main cacao pathogens in the tropical. Besides species of the Malvaceae family, the fungal has emerged in host species of the Solanaceae, Malpighiaceae, and Bignoniaceae families. This host range is still poorly understood. The genome sequencing of M. perniciosa strict sense isolates supports bioinformatics and comparative genomics approaches as important tools in studying the biology and evolution of M. perniciosa, herein focuses on genome size. The genomic sizes of six M. perniciosa isolates (representatives of wild nightshade, cultivated nightshade, and cocoa) were estimated from raw genomic sequencing data using KmerGenie v1.7051 software. This prediction showed a variation of the genomic size of 38.19 to 51.53Mb. In general, M. perniciosa from Solanaceous hosts showed a smaller genome size than isolates from cacao, except for one isolate from bell pepper that showed the biggest size. It was proven that there is cross-infection between cocoa isolates and cultivated nightshade through pathogenicity studies. However, those from wild nightshade are not pathogenic to cocoa. This variation in genome size may reflect the evolution in the pathogenicity of this fungus, through several mechanisms. In particular, organisms with bigger genomes tend to have more genes, more and longer introns, and more transposable elements than organisms with smaller genomes. Our findings indicate that genome size variation is an important adaptation during the evolution of M. perniciosa.