Injection into the injured spinal cord of peptide amphiphile (PA) molecules that self-assemble and display the laminin epitope IKVAV at high density improved functional recovery after spinal cord injury (SCI) in two different species, rat and mouse, and in two different injury models, contusion and compression. The improvement required the IKVAV epitope and was not observed with the injection of an amphiphile displaying a non-bioactive sequence. To explore the mechanisms underlying these improvements, the number of serotonergic fibers in the lesioned spinal cord was compared in animals receiving the IKVAV-PA, a non-bioactive PA (PA control), or sham injection. Serotonergic fibers were distributed equally in all three groups rostral to the injury, but showed a significantly higher density caudal to the injury site in the IKVAV PA injected group. Further, this difference was not present in the subacute phase following injury but appeared in the chronically injured cord. The IKVAV PA injected groups also trended higher both in the total number neurons adjacent to the lesion and in the number of long propriospinal tract connections from the thoracic to the lumbar cord. IKVAV PA injection did not alter myelin thickness, total axon number caudal to the lesion, axon size distribution, or total axon area. Since serotonin can promote stepping even in complete transection models, the improved function produced by the IKVAV PA treatment may reflect the increased serotonergic innervation caudal to the lesion in addition to the previously demonstrated regeneration of motor and sensory axons through the lesion.