It is recognized that elucidation of chemical structure at molecular level is important to develop new application of coal. As a result of various experiments, it has been clarified that the coal molecular consists of the following three components, the aromatic class cluster, the bridge connecting the aromatic class cluster, and the end permutation radical. Chemists have to construct theses components by hand, utilizing their empirical knowledge. It is desired to support this time consuming work with computers.In this paper, we propose a method of constructing the molecular structure using the genetic algorithm(GA). In this method, the chromosomes are expressed in the form of graphs. At the crossover operation, partial graph of one parent is kept and the nodes in the rest graph inherit connectivity of nodes from the other parent. The evaluation function is determined based on the heuristics of chemists as 'the density of the coal molecular is uniform averagely'. As a result of some experiments with structures constructed from real coal data, it was clarified that our method was effective to estimate the coal molecular structure.