Endoglucanases are involved in the initial stages of cellulose breakdown--an essential step in the bioprocessing of lignocellulosic plant materials into bioethanol. Although these enzymes are economically important, we currently lack a basic understanding of how some endoglucanases can sustain their ability to function at elevated temperatures needed for bioprocessing, while others with the same fold cannot. In this study, we present a detailed comparative analysis of both thermophilic and mesophilic endoglucanases in order to gain insights into origins of thermophilicity. We used the CAZy (Carbohydrate-Active enZymes) database to build our endoglucanase protein data sets and analyzed their sequences and structures. Our results demonstrate that thermophilic endoglucanases and their mesophilic counterparts differ significantly in their amino acid compositions. Strikingly, these compositional differences are specific to protein folds and enzyme families and lead to modification in hydrophobic, aromatic, and ionic interactions in a fold-dependent fashion. However, when it comes to thermophilicity, there is a caveat of applying general heuristic rules to specific proteins: although thermophilicity in endoglucanases is usually conferred through altering amino acid composition, in some cases even a single-point mutation is sufficient to convert a mesophilic protein into a thermophilic protein. Here, we provide fold-specific guidelines to control thermophilicity in endoglucanases that will make production of biofuels from plant biomass more efficient.