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Identifying functional enzymes for the catalysis of specific biochemical reactions is a major bottleneck in the de novo design of biosynthesis and biodegradation pathways. Conventional methods based on microbial screening and functional metagenomics require long verification periods and incur high experimental costs; recent data-driven methods apply only to a few common substrates. To enable rapid and high-throughput identification of enzymes for complex and less-studied substrates, we propose a robust enzyme's substrate promiscuity prediction model based on positive unlabeled learning. Using this model, we identified 15 new degrading enzymes specific for the mycotoxins ochratoxin A and zearalenone, of which six could degrade >90% mycotoxin content within 3 h. We anticipate that this model will serve as a useful tool for identifying new functional enzymes and understanding the nature of biocatalysis, thereby advancing the fields of synthetic biology, metabolic engineering, and pollutant biodegradation.