Cross-genome comparative transcriptome analyses were previously conducted using the sequenced Streptomyces coelicolor genome microarrays to understand the genetic nature of doxorubicin (DXR) and daunorubicin (DNR) overproducing industrial mutant (OIM) of Streptomyces peucetius. In this previous work, a whiB-like putative transcription factor (wblA ( sco )) was identified as a global antibiotic down-regulator in S. coelicolor (Kang et al., J Bacteriol 189:4315-4319, 2007). In this study, a total genomic DNA library of a DXR/DNR-overproducing S. peucetius OIM was constructed and screened using wblA ( sco ) as a probe, resulting in the isolation of a wblA ortholog (wblA ( spe )) that had 95% amino acid identity to wblA ( sco ). Gene disruption of wblA ( spe ) from the S. peucetius OIM resulted in an approximately 70% increase in DXR/DNR productivity, implying that the DXR/DNR production in the S. peucetius OIM could be further improved via comparative transcriptomics-guided target gene manipulation. Furthermore, several putative wblA ( spe ) -dependent genes were also identified using S. coelicolor interspecies DNA microarray analysis between the S. peucetius OIM and wblA ( spe )-disrupted S. peucetius OIM. Among the genes whose expressions were significantly stimulated in the absence of wblA ( spe ), the overexpression of a conserved hypothetical protein (SCO4967) further stimulated the total production of DXR/DNR/akavinone by 1.3-fold in the wblA ( spe )-disrupted S. peucetius OIM, implying that the sequential genetic manipulation of target genes identified from interspecies comparative microarray analysis could provide an efficient and rational strategy for Streptomyces strain improvement.