© Springer International Publishing Switzerland 2015. Decentralized distributed systems, such as grids, clouds or networks of sensors, have been widely investigated recently. An important nature of such systems is the heterogeneity of their resources; in order to archive the availability, scalability and flexibility.As a consequence, managing the systems to meet requirements is obviously a nontrivial work. The issue is evenmore challenging in term of job scheduling when the task dependency within each job exists. In this paper, we address such problem of job scheduling, so called workflow-based job scheduling, in the decentralized distributed systems with heterogeneous resources. As such problem is proven to be an NP-complete problem, an efficient heuristic algorithm to address this problem is proposed. The algorithm is based on an observation that the heterogeneity of the resources can affect the execution time of the scheduling.We compare the effectiveness and efficiency of the proposed algorithm with a baseline algorithm. The result shows that our algorithm is highly effective and efficient for the scheduling problem in the decentralized distributed system with heterogeneous resources environment both in terms of the solution quality and the execution time respectively.