Inulinase is an enzyme produced by plants and several microorganisms, including fungi, to hydrolyze the β-2,1 glycosidic linkages present in some oligosaccharides to produce fructose and glucose. This enzyme, in conjunction with invertases, levanases, and two types of 1-fructosyl transferases have been described as members of the glycosyl hydrolases (family 32), the most diverse group of enzymes used by microbes for biomass degradation. As being part of the same clan, they have common evolutionary origin sharing the most important functional characteristics. Recently, a xerophylic fungi strain isolated from Mexican semi-desert, Penicillium citrinum ESS has been reported as inulinase producer, which could have greater stability than other enzymes due to a metabolic machinery adapted to typical temperature changes in this region. To continue the understanding of action mechanisms of these enzymes and to establish evolutionary relationships within this family, in the present study, phylogenetic analyses were used to analyze amino acid sequences coding fungal and yeast glycoside hydrolases of family 32, including the new sequenced inulinase of P. citrinum ESS. It was possible to elucidate the action mechanism of fungal glycoside hydrolases in present study and to classify inulinase from P. citrinum ESS as an exo-inulinase on the basis of their amino acid sequence phylogenetic affinities.