Aims The aim of this work was to characterize and apply a polygalacturonase of Penicillium janthinellum new strain VI2R3M. Methods and Results The polygalacturonase obtained from P. janthinellum VI2R3M was incubated in cultures of passion fruit peel and was partially purified by ion-exchange chromatography and gel filtration. The enzyme showed a relative molecular mass of 102 center dot 0 kDa, maximum activity at pH 5 center dot 0, temperature of 50 degrees C, 100% stablity at 50 degrees C and 80% stablity at pH 3 center dot 0-5 center dot 0. The apparent K-m, V-max and K-cat values for hydrolyzing polygalacturonic acid were 2 center dot 56 mg ml(-1), 163 center dot 1 U mg(-1) and 277 s(-1) respectively. The polygalacturonase presented exo activity and was activated by Mg2+. The juices treated with polygalacturonase presented increases in transmittance with reduction in colour. Conclusions The results suggest that the new lineage P. janthinellum VI2R3M presents a high yield of an exo-polygalacturonase induced by agro-industrial residues, with excellent activity and stability in acidic pH and at 50 degrees C. Significance and Impact of the Study The use of agro-industrial residue to obtain the polygalacturonase can contribute to a decrease enzyme production cost. The results of the activity, stability to acidic pH and excellent performance in the clarification of juices show that the enzyme is promising for industrial application.