The purpose of this report is to understand the effects of hybrid zone architecture and genetic drift on cytonuclear genotypic disequilibria. We also study the exact dynamics of the expected values of the cytonuclear genotypic disequilibria for both the homozygotes and heterozygotes in a finite population containing reproductively isolated subpopulations under random drift alone and random drift along with mutation, respectively. We study the dynamics of the between-population component of the disequilibrium for the homozygotes. The dynamics of the variances of these disequilibria under the random drift model are studied by Monte Carlo simulations. The asymptotic formulas for both the expectations and variances are obtained. The results are contrasted with those for a single undivided population and their biological significances are discussed. Approximate normality of the disequilibria measures are also demonstrated by Monte Carlo simulations.