Knowledge on the evolution of aminoacyl-tRNA synthetases is crucial to studies on the origins of life. The relationships between the different aminoacyl-tRNA synthetase specificities in prokaryotic organisms are studied in this work. We reconstructed the ancestor sequences and the phylogenetic relationships utilizing the Maximum Likelihood method. The results suggest that in class I the evolution of the N-terminal segment was strongly influenced by the amino acid hydropathy in both domains of prokaryotes. The results for the C-terminal segments of class I were different in the two domains, indicating that its evolution was strongly influenced by the specific types of tRNA modification in each domain. The class II groups in Archaea were more heterogeneous with respect to the hydropathy of amino acids, indicating the interference of other influences. In bacteria, the configuration was also complex but the overall consensual division in two groups was maintained, group IIa forming a single branch with the five hydroapathetic amino acid specificities and group IIb containing the specificities for the moderately hydrophobic together with the hydrophilic amino acids. It is indicated that the aminoacyl-tRNA synthetase in both domains were subjected to different selective forces in diverse parts of the proteins, resulting in complex phylogenetic patterns.