The hybrid CMOS molecular (CMOL) circuit, which combines complementary metal–oxide–semiconductor (CMOS) components with nanoscale wires and switches, can exhibit significantly improved performance. In CMOL circuits, the nanodevices, which are called cells, should be placed appropriately and are connected by nanowires. The cells should be connected such that they follow the shortest path. This paper presents an efficient method of cell allocation in CMOL circuits with the hybrid CMOS/nanodevice structure; the method is based on a cultural algorithm with chaotic behavior. The optimal model of cell allocation is derived, and the coding of an individual representing a cell allocation is described. Then the cultural algorithm with chaotic behavior is designed to solve the optimal model. The cultural algorithm consists of a population space, a belief space, and a protocol that describes how knowledge is exchanged between the population and belief spaces. In this paper, the evolutionary processes of the population space employ a genetic algorithm in which three populations undergo parallel evolution. The evolutionary processes of the belief space use a chaotic ant colony algorithm. Extensive experiments on cell allocation in benchmark circuits showed that a low area usage can be obtained using the proposed method, and the computation time can be reduced greatly compared to that of a conventional genetic algorithm.