Unlike using the sequence-based representation for a chromosome in previous genetic algorithms for Bayesian structure learning, we proposed a matrix representation-based genetic algorithm. Since a good chromosome representation helps us to develop efficient genetic operators that maintain a functional link between parents and their offspring, we represent a chromosome as a matrix that is a general and intuitive data structure for a directed acyclic graph(DAG), Bayesian network structure. This matrix-based genetic algorithm enables us to develop genetic operators more efficient for structuring Bayesian network: a probability matrix and a transpose-based mutation operator to inherit a structure with the correct edge direction and enhance the diversity of the offspring. To show the outstanding performance of the proposed method, we analyzed the performance between two well-known genetic algorithms and the proposed method using two Bayesian network scoring measures.