Information on the gene effects governing the inheritance of traits is very important for crop breeding and germplasm management. The objective of this study was to estimate genetic effects for total anthocyanin content in the tassel of small-ear waxy corn. Six generations (P1, P2, F1, F2, BC11, and BC12) were developed from two crosses of small-ear waxy corn (TB1 × TW1 and TC1 × TB3). TB1 and TB3 had purple tassels, and TW1 and TC1 had green tassels. All generations of each cross were evaluated under field conditions in the rainy season of 2017 and the dry season of 2017/2018. Season, generation, and their (S × G) interaction had significant effects in TB1 × TW1 and TC1 × TB3. For both crosses, generation had the largest effect on the total variance followed by season and S × G interaction. A three-parameter model was adequate for estimating genetic effects. Additive gene effects were significant for controlling the inheritance of total anthocyanin concentration in tassels. The significant additive effect suggested that selection for anthocyanin content in early generations will be effective, and hybrid combinations obtained from superior parental lines with unrelated genetic backgrounds may be an effective option to increase anthocyanin concentration in the tassels of small-ear waxy corn.