Cladosporium spp. as one of the largest and most heterogeneous genera of hyphomycetes, are widely distributed worldwide. This genus is usually adaptable to a wide variety of extreme environments. However, only several genomes of Cladosporium genus have been publicly released. Two years ago, we found for the first time that Cladosporium velox could cause cotton boll disease and lead to stiffness and cracking boll in Xinjiang, China. Herein, we provide a high-quality reference genome for the C. velox strain C4 isolated from cotton boll in Xinjiang, China. This resource will contribute to future research that aims to elucidate the genetic basis of C. velox pathogenicity.