Abstract Background One of the goals of the Systems Biology community is to have a detailed map of all biological interactions in an organism. One small yet important step in this direction is the creation of biological networks from post-genomic data. Bayesian networks are a very promising model for the inference of regulatory networks in Systems Biology. Usually, Bayesian networks are sampled with a Markov Chain Monte Carlo (MCMC) sampler in the structure space. Unfortunately, conventional MCMC sampling schemes are often slow in mixing and convergence. To improve MCMC convergence, an alternative method is proposed and tested with different sets of data. Moreover, the proposed method is compared with the traditional MCMC sampling scheme. Results In the proposed method, a simpler and faster method for the inference of regulatory networks, Graphical Gaussian Models (GGMs), is integrated into the Bayesian network inference, trough a Hierarchical Bayesian model. In this manner, information about the structure obtained from the data with GGMs is taken into account in the MCMC scheme, thus improving mixing and convergence. The proposed method is tested with three types of data, two from simulated models and one from real data. The results are compared with the results of the traditional MCMC sampling scheme in terms of network recovery accuracy and convergence. The results show that when compared with a traditional MCMC scheme, the proposed method presents improved convergence leading to better network reconstruction with less MCMC iterations. Conclusions The proposed method is a viable alternative to improve mixing and convergence of traditional MCMC schemes. It allows the use of Bayesian networks with an MCMC sampler with less iterations. The proposed method has always converged earlier than the traditional MCMC scheme. We observe an improvement in accuracy of the recovered networks for the Gaussian simulated data, but this improvement is absent for both real data and data simulated from ODE.