Anthocyanins of pigmented corn become a topic of increasing interest recently due to consumer awareness of their various health benefits. A better understanding on the gene effects to anthocyanin is an important for high antioxidants breeding programs. The objective of the present study was to determine gene effect controlling of anthocyanin content in purple waxy corn kernel and cob by generation mean analysis. For the cross of KND 10-4P (P1) × BW (P2), F2, and backcross generations were developed. All generations were planted in the randomized complete block design (RCB) with 3 replications at the Khon Kaen University, Thailand. Genetic analysis showed that the additive gene effects appeared to be a major contribution to the inheritance for pelargonidin-3-glucosid and peonidin-3-glucoside in the purple corn cob, indicate that selection for these anthocyanins is made at early breeding generations may be possible. Moreover, dominance and dominance × dominance epistatic effects were important for all studied traits in the corn kernel and cyanidin-3-glucoside in purple corn cob so initial selection can be carried out in large populations of later generations with increased homozygosity.