The accuracy of protein biosynthesis generally rests on a family of 20 aminoacyl‐tRNA synthetases, one for each amino acid. In bacteria, archaea and eukaryotic organelles, the formation of Gln‐tRNAGln is prevalently accomplished by a transamidation pathway, aminoacylation of tRNAGln with Glu by glutamyl‐tRNA synthetase (GluRS) followed by a tRNA‐dependent transamidation of Glu from Glu‐tRNAGln. A few bacterial species, such as Escherichia coli, possess a glutaminyl‐tRNA synthetase (GlnRS), responsible for Gln‐tRNAGln formation. Phylogenetic analysis of the GluRS or GlnRS families (GlxRS) suggested that GlnRS has a eukaryotic origin and was horizontally transferred to a restricted set of bacteria. We have now isolated an additional GlnRS gene from the plant Lupinus luteus and analyzed in more details the modular architecture of the paralogous enzymes GluRS and GlnRS, starting from a large data set of 33 GlxRS sequences. Our analysis suggests that the ancestral GluRS‐like enzyme was solely composed of the catalytic domain bearing the class‐defining motifs of aminoacyl‐tRNA synthetases, and that the anticodon‐binding domain of GlxRSs was independently acquired in the bacteria and archaea branches of the universal tree of life, the eukarya sub‐branch arising as a sister group of archaea. The transient capture of UAA and UAG codons could have favored the emergence of a GlnRS in early eukaryotes.