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Estimation of distribution algorithms are a promising method in evolutionary computation. In the estimation of distribution algorithms, instead of using conventional crossover and mutation operations, probabilistic models are used to sample the genetic information in the next population. Although the use of probabilistic models enables EDAs to have several schema simultaneously, it sometimes causes worse performance due to converse schemata. In this paper, estimation of distribution algorithms with niche separation mechanism is proposed. Coexistence schemata are also newly introduced, where schemata at the same loci but converse information. The proposed method splits population into two subpopulations if such coexistence schemata are found. One of subpopulations is used to constitute the next generation while the probabilistic model of another subpopulation is enqueued. The queued probabilistic model is used if the current population is converged. The experimental results on max-sat problems and Ising spin glass problems show the effectiveness of the proposed method.