Avermectin and its analogues are produced by the actinomycete
Streptomyces avermitilis
and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene,
aveR
, were up-regulated in the high-producing strain. The upstream promoter region of
aveR
was predicted and proved to be directly recognized by
σhrdB
in vitro. A mutant library of
hrdB
gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved
hrdB
expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of
aveR
was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the
hrdB
gene can not only elicit the overexpression of
aveR
but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems.