Petunia (Petunia hybrida) is one of the important plants in horticultural industry. This plant is being used as a model ornamental plant and is one of the most important plants in floriculture market. Flavonoids are the main pigment in this plant. So, genetic engineering with the goal of color alteration in petunia is focused on flavonoids. To gain a global perspective on genes differentially expressed in petunia’s flowers pigment pathway, we investigated the expression of chalcone isomerase (chi) as an essential gene in biosynthesis pathway of pigment production in different types of flower color of petunia and various stages of flowering in this plant. Also, we measured the concentration of total flavonoids, anthocyanins and naringenin to evaluate the probably relationship between the expression profile of chi gene and the concentration of mentioned pigments. The results indicated that chalcone isomerase expression had different profile in different petal color of P. hybrida. So that, the most chi expression observed in red petunia flowers. Naringenin concentrations was the most value in this color flower. In comparison of flowering stages, stage 1, had the most expression. In other words, when the flowers fully closed (bud stage), chi expression and concentration was in the highest value. Our results showed that chi is a key gene in pigment biosynthesis pathway so that in absence of this gene, pigment pathway will be stopped. Identification of effective genes in different pathways of secondary metabolite production will assist in accurate selection of genes for genetically modification of pathways and production of various metabolites. تفاصيل المقالة