<jats:title>Abstract</jats:title><jats:p>Aldgamycins are 16‐membered macrolide antibiotics with a rare branched‐chain sugar <jats:sc>d</jats:sc>‐aldgarose or decarboxylated <jats:sc>d</jats:sc>‐aldgarose at C‐5. In our efforts to clone the gene cluster for aldgamycins from a marine‐derived <jats:italic>Streptomyces</jats:italic> sp. HK‐2006‐1 capable of producing both aldgamycins and chalcomycins, we found that both are biosynthesized from a single gene cluster. Whole‐genome sequencing combined with gene disruption established the entire gene cluster of aldgamycins: nine new genes are incorporated with the previously identified chalcomycin gene cluster. Functional analysis of these genes revealed that <jats:italic>almDI</jats:italic>/<jats:italic>almDII</jats:italic>, (encoding α/β subunits of pyruvate dehydrogenase) triggers the biosynthesis of aldgamycins, whereas <jats:italic>almCI</jats:italic> (encoding an oxidoreductase) initiates chalcomycins biosynthesis. This is the first report that aldgamycins and chalcomycins are derived from a single gene cluster and of the genetic basis for bifurcation in their biosynthesis.