In several archaea of the Euryarchaeota, the glycolytic flux proceeds through a modified version of the Embden-Meyerhof pathway, where the phosphofructokinase and glucokinase enzymes use ADP as the phosphoryl donor. These enzymes are homologous to each other. In the hyperthermophilic methanogenic archaeon Methanocaldococcus jannaschii, it has been possible to identify only one homolog for these enzymes, which shows both ADP-dependent glucokinase and phosphofructokinase activity. This enzyme has been proposed as an ancestral form in this family. In this work we studied the evolution of this protein family using the Bayesian method of phylogenetic inference and real value evolutionary trace in order to test the ancestral character of the bifunctional enzyme. Additionally, to search for specificity determinants of these two functions, we have modeled the bifunctional protein and its interactions with both sugar substrates using protein-ligand docking and restricted molecular dynamics. The results show that the evolutionary story of this family is complex. The root of the family is located inside the glucokinase group, showing that the bifunctional enzyme is not an ancestral form, but could be a transitional form from glucokinase to phosphofructokinase, due to its basal location within the phosphofructokinase group. The evolutionary trace and the molecular modeling experiments showed that the specificity for fructose 6-phosphate is mainly related to the stabilization of a negative charge in the phosphate group, whereas the specificity for glucose is related to the presence of some histidines instead of glutamines/asparagines and to the interaction of this ligand with a glutamic acid residue corresponding to Glu82 in the bifunctional enzyme.