Streptomyces are our primary source of antibiotics, produced concomitant with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control the initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control the differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σWhiG). We present the structure of the RsiG-(c-di-GMP)2-sWhiG complex, revealing an unusual partially intercalated c-di-GMP dimer bound at the RsiG-sWhiG interface. RsiG binds c-di-GMP in the absence of sWhiG employing a novel E(X)3S(X)2R(X)3Q(X)3D motif repeated on each helix of a coiled-coil. Further studies demonstrate c-di-GMP is essential for RsiG to inhibit σWhiG. These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.