Streptomyces avermitilis is a well known organism producing avermectin antibiotics, and has been utilized as an industrial host for oxidation bioconversion processes. Recently, gene screening strategies related to bioconversions have received much focus, as attempts are made to optimize oxidation and biodegradation pathways to maximize yield and productivity. Here, we have demonstrated the oxidative metabolisms of three molecules, daidzein, p-coumaric acid and mevastatin, where S. avermitilis converted each substrate to 3',4',7-trihydroxyisoflavone, caffeic acid and hydroxyl-mevastatin to yield 9.3, 32.5 and 15.0 %, respectively. Microarray technology was exploited to investigate genome-wide analysis of gene expression changes, which were induced upon the addition of each substrate. Cytochrome P450 hydroxylases (pteC, cyp28 and olmB), diooxygenases (xylE, cdo1 and putatives) and LuxAB-like oxygenase were identified. One of them, cyp28, was indeed a gene encoding P450 hydroxylase responsible for the oxidative reaction of daidzein. Furthermore, possible electron transfer chain (fdrC → pteE → pteC) supporting cytochrome P450 dependent hydroxylation of daidzein has been suggested based on the interpretation of expression profiles. The result provided a potential application of transcriptomic study on uncovering enzymes involved in oxidative bioconversions of S. avermitilis.