The selection of the novel pectinesterase (PE) producing strains is an important step in their biotechnological application. The present work displays the purposeful multistage selection of strains with the increased ability to synthesize extracellular PE among 700 filamentous fungal collection cultures belonging to 45 genera and 93 species. A scheme of targeted multistage screening of PE producers has been developed. At the first stage of the screening 23 potentially active strains belonging to the genera Penicillium, Fusarium, Aspergillus, Rhizopus, Gliocladium, etc., were selected. Strains of the Trichoderma, Cochliobolus, Cladosporium and Thielavia genera not yet described as PE-active ones were selected. The P. funiculosum species (0.28-0.56 units/ml) possessed higher ability to synthesize PE. High level of the PE activity was revealed in P. rubrum (0.37 units/ml). No correlation between the level of fungal biomass accumulation on pectin-containing medium and the level of their PE activity was observed. A principal chance of the fungal PE substitution for some chemical reagents at the stage of demethoxylation of the pectin-containing raw materials should be noted. The technology of the fungal PE application for production of the low-degree methoxylated pectin is under development. Such pectin is necessary for the low-calorie jellfying products in the food industry and in medicine as a preventive agent removing the toxic substances from the human body.