The junB locus contains nine flanking evolutionarily conserved sequences (FECS) that share 72% to 91% sequence identity between human and mouse. These FECS encompass the same regions of flanking DNA necessary for maximal mitogenic induction of junB. Most of the cis elements reported to date that affect junB regulation also reside within FECS. These observations suggest that the persistence of FECS through evolution reflects a necessary role in junB transcriptional regulation. In this report, we identify specific regulatory cis elements within junB FECS II and III and provide a quantitative analysis of the contribution made by these sequences to junB induction. These cis elements include a Serum Response Element (SRE), two Ets sites previously unrecognized as contributing to junB expression, and two novel Ets-linked motifs (ELMs). In general, mutating any single element significantly impairs junB induction. Moreover, the same mutations alter the structure of junB 5' flanking DNA within chromatin. Collectively, these results suggest that multiple proteins bound within FECS confederate to form a functional promoter complex, the activity of which is dependent upon a specific chromatin architecture.