We propose a crossover method to combine complexly overlapping building blocks (BBs). Although there have been several techniques to identify linkage sets of loci o form a BB [4, 6, 7, 10, 11], the way to to realize effective crossover from the linkage information from such techniques has not been studied enough. Especially for problems with overlapping BBs, a crossover method proposed by Yu et al. [13] is the first and only known research, however it cannot perform well for problems with complexly overlapping BBs due to insufficient variety of crossover sites. In this paper, we propose a crossover method which examines values of given parental strings minutely and defines which variables are exchanged to produce new and different strings without increasing BB disruptions as much as possible. The method is combined with a scalable linkage identification technique to construct an efficient algorithm for problems with overlapping BBs. We design test functions with controllable complexit...