For optimization problems with irregular and complex multimodal landscapes, Estimation of Distribution Algorithms (EDAs) suffer from the drawback of premature convergence similar to other evolutionary algorithms. In this paper, we propose an adaptive niching EDA based on Affinity Propagation (AP) clustering analysis. The AP clustering is used to adaptively partition the niches and mine the searching information from the evolution process. The obtained information is successfully utilized to improve the EDA performance by using a balance niching searching strategy. Two different categories of optimization problems are used to evaluate the proposed adaptive niching EDA. The first one is solving three benchmark functional multimodal optimization problems by a continuous EDA based on single Gaussian probabilistic model; the other one is solving a real complicated discrete EDA optimization problem, the HP model protein folding based on k-order Markov probabilistic model. Simulation results show that the proposed adaptive niching EDA is an efficient method.