Serratia sp. ATCC39006 (S39006) is a rod-shaped, motile, Gram-negative phytopathogenic bacterium. It is the only enterobacterium known to make gas vesicles (GVs) naturally. GVs are proteinaceous, intracellular organelles used by bacteria to enable upward flotation in aquatic environments. S39006 also produces various secondary metabolites, including the tripyrrole red-pigmented antibiotic, 2‐methyl‐3‐pentyl‐6‐methoxyprodigiosin (prodigiosin; a prodiginine) and the β-lactam antibiotic, 1-carbapen-2-em-3-carboxylic acid (a carbapenem). The production and regulation of GV assembly is a complex process, which is part of a wider regulatory network affecting various phenotypes, including the carbapenem and prodigiosin antibiotics. The present study aimed to identify genes involved in pleiotropic co-regulation of GV production and biosynthesis of the carbapenem and prodigiosin antibiotics. To identify new regulatory genes, random transposon mutagenesis was employed. Mutants defective in the ribose operon repressor (rbsR), topoisomerase I (topA) and the preQ0 transporter (orf9) were identified from a comprehensive mutant library. The rsbR mutant was defective in GV, carbapenem and prodigiosin production, but showed increased swimming and swarming motility. Additionally, a siderophore, cellulase and plant virulence were reduced in the mutant. In the topA mutant, prodigiosin was greatly elevated but reduction was observed in carbapenem, cellulase, pectate lyase, N-BHL and siderophore production, and motility. The orf9 gene also had multiple physiological effects in S39006. Reduced GV, prodigiosin and cellulase production, but increased swimming and swarming motilities, were observed in the orf9 mutant. To understand the role of RbsR as a global regulator in S39006, comparative quantitative proteomic analysis was employed. Proteins involved in GV biogenesis, motility, antibiotic and cellulase production, as well as five previously identified transcriptional regulators, were affected in the mutant. With molecular genetic characterisation and proteomic analysis, this study identified three regulatory genes, rsbR, topA, and orf9 that are not only important in modulating GV morphogenesis (and flotation) but are also pleiotropic for control of biosynthesis of the secondary metabolites, some secreted enzymes and motility.