Through cloning and analyzing the expression of the CCoAOMT and SAMS genes in Impatiens hawkeri， we provided a theoretical basis for understanding the biosynthesis of 2-methoxy-1，4-naphthoquinone （MNQ）. Based on the quantification of MNQ content and the transcriptome profile datasets in I. hawkeri ， one CCoAOMT and two SAMS genes of I. hawkeri were identified and cloned， named IhCCoAOMT， IhSAMS1 and IhSAMS2. Three treatments including light， dark and DHNA（1，4-dihydroxy-2-naphthoate） could promote the MNQ accumulation， with best performance under dark culture. The full-length coding sequence of IhCCoAOMT is 729 bp and encodes 242 aa containing the AdoMet_MTases superfamily domain. The CDS of IhSAMS1 and IhSAMS2 are 1179 bp and 1173 bp， which encode 393 aa and 391 aa， respectively. Their deduced proteins were predicted with the S-AdoMet_synt superfamily domain. Phylogenetic analysis showed that IhCCoAOMT was closely related to I. glandulifera. IhSAMS1 and IhSAMS2 of I. hawkeri may be paralogous genes. These genes were detected with transcripts at four culture periods under three treatments. The expression level of IhCCoAOMT increased in dark culture and DHNA treatment， and the highest expression was found on 60 days post dark culture. The expression levels of IhSAMS1 and IhSAMS2 were decreased in dark culture and DHNA treatment. The expression level of IhSAMS1 was higher than that in DHNA treatment， and a higher expression of IhSAMS2 was observed under dark culture treatment. Collectively， IhCCoAOMT was speculated with a key role at the late stage of MNQ treatment， while IhSAMS1 and IhSAMS2， especially for IhSAMS2， possibly played roles at the early stage.