Gray mold disease, mainly caused by Botrytis elliptica (Berk.) Cooke and Botrytis cinerea Pers., leads to severe losses in lily cut flower and bulb production. MYC2 is a critical regulator of the activation of jasmonate-mediated defense responses in plants; however, information about the lily MYC2 gene is limited. Therefore, functional characterization of MYC2 in lily, especially its role in plant immune responses, should be performed. Here, significant differences between the Botrytis-resistant Lilium hybrid ‘Sorbonne’ and the Botrytis-susceptible ‘Tresor’ were found following B. cinerea inoculation, as indicated by jasmonic acid (JA) and JA-isoleucine (JA-Ile) accumulation and related gene expression. More JA and JA-Ile were detected in ‘Sorbonne’ than in ‘Tresor’ following fungal inoculation, and higher transcript levels of JA biosynthesis genes (LhAOS, LhAOC, and LhOPR3) and a signaling gene (LhCOI1) were detected in ‘Sorbonne’ than in ‘Tresor’. In contrast, expression of the critical signaling regulator LhMYC2 was higher in ‘Tresor’ than in ‘Sorbonne’. LhMYC2 was then isolated from ‘Sorbonne’ and found to be similar to several plant MYC2 homologs that have pivotal roles in JA signaling. The expression of LhMYC2 increased significantly in response to JA and salicylic acid (SA) in ‘Sorbonne’. Ectopic expression of LhMYC2 in Arabidopsis resulted in greater susceptibility to B. cinerea than that observed in wild-type plants. This susceptibility was coupled with the transcriptional changes in SA- and JA-responsive genes. Overall, our findings indicate that LhMYC2 plays a negative role in Arabidopsis resistance to B. cinerea.