Epigenetic variation plays a role in developmental gene regulation and responses to the environment. An efficient interaction of zeatin induced cytosine methylation and secondary compounds has been displayed for the first time in tissue-culture shoots of lingonberry (Vaccinium vitis-idaea) in vitro, in vivo and its cutting-cultivar Erntedank. Through MSAP assay, we observed highest methylated sites in leaf regenerants (LC1) from all primer combinations (108 bands), with their highest variation in secondary metabolites. We measured that four tissue-culture plants showed higher methylation bands than cutting propagated donor plants (ED) which exhibited 79 bands of methylation, which is comparatively low. On the other hand, we observed the highest total phenolic content in node culture-derived greenhouse grown plants, NC3 but leaf culture-derived greenhouse grown plants, LC1 represented low phenolic content. Our study showed more methylation in micropropagated plants (NC1, NC2, NC3, LC1) than those derived from cutting propagated ED plants, where methylation was not present. On the contrary, we observed higher secondary metabolites in ED plants but comparatively less in micropropagated shoots (NC1, NC2) and plants (NC3, LC1). Our study displayed that higher methylation sites observed in micropropagated plants possessed less amount of secondary metabolites.