Abstract The aim of the present study was to understand the molecular structure and evolutionary mechanisms of peptidoglycan hydrolases (PGHs) in lactic acid bacteria (LAB) and their phages, thereby making them more widely applicable for research purposes. Forty-nine PGHs, 42 from LAB and the rest from their bacteriophages, were analyzed using bioinformatics methods. PGHs comprised mainly muramidase (i.e., lysozyme) and amidase and, rarely, peptidase and N-acetyl-β-glucosaminidase. Muramidases, but not members of the endolysin–autolysin family, were predicted to express LysM motifs (a common protein motif that binds peptidoglycans); however, it was not expressed by all muramidases. Muramidases from Lactococcus phages expressed two LysM motifs, whereas the number expressed by Lactobacillus bacteriophages varied widely. Similarly, muramidases contained a signal peptide, whereas members of the endolysin–autolysin super-family, amidases and peptidases, did not. Multiple sequence alignment and evolution analyses revealed that muramidases encoded by different bacteriophages showed a close relationship with those expressed by their respective host bacteria.