A yellow green peel mutant (ygp) in cucumber was caused by a mutation in Csa2G352940 encoding MYB36 transcription factor. Peel color is one of the important agronomic traits of cucumber (Cucumis sativus L.). However, studies on the molecular regulation mechanism of peel color in cucumber are few. In this study, a cucumber yellow green peel mutant (ygp) of cucumber mutagenized with ethylmethylsulfone by using a wild type cucumber with dark green peel was identified. Pigment measurements indicated that the chlorophyll content of the ygp mutant was less than that of the wild type. Genetic analysis revealed that the phenotype of the ygp mutant was monogenic recessive inheritance. MutMap and genotyping results demonstrated that Csa2G352940 (CsMYB36), encoding the transcription factor MYB36, was the causal gene of the ygp mutant in cucumber. CsMYB36 was downregulated in the fruit of the ygp mutant. Transcriptome profile analysis of the fruit peel of the ygp mutant identified 92 candidate genes including genes that encode Casparian strip (CsCASP1) and pigment synthesis protein (CsMYC2) involved in peel color development in cucumber. CsMYB36 may regulate yellow green coloration in cucumber by interacting with these genes. Overall, these results showed that CsMYB36 can regulate the yellow green peel coloration in cucumber.