This paper reports the hybridization of the artificial bee colony (ABC) and a genetic algorithm (GA), in a hierarchical topology, a step ahead of a previous work. We used this parallel approach for solving the protein structure prediction problem using the three-dimensional hydrophobic-polar model with side-chains (3DHP-SC). The proposed method was run in a parallel processing environment (Beowulf cluster), and several aspects of the modeling and implementation are presented and discussed. The performance of the hybrid-hierarchical ABC-GA approach was compared with a hybrid-hierarchical ABC-only approach for four benchmark instances. Results show that the hybridization of the ABC with the GA improves the quality of solutions caused by the coevolution effect between them and their search behavior.where RG aa can be either RG H or RG P , when considering only hydrophobic or polar amino acids; x i , y i and´i are the coordinates of the i-th SC of type "aa" of the protein, either H of P; X , Y and Z are the average of all x i , y i , and´i ; and N aa is the number of SCs of type "aa". Figure 2. Example of genotype-phenotype decoding.