Motor behavior requires the balanced production and integration of a variety of neural cell types. Motor neurons are positioned in discrete locations in the ventral spinal cord, targeting specific muscles to drive locomotive contractions. Specialized spinal interneurons modulate and synchronize motor neuron activity to achieve coordinated motor output. Changes in the ratios of spinal interneurons could drastically alter motor output by tipping the balance of inhibition and excitation onto target motor neurons. Importantly, individuals with Fragile X syndrome (FXS) and associated autism spectrum disorders often have significant motor challenges, including repetitive behaviors and epilepsy. FXS stems from the transcriptional silencing of the gene Fragile X Messenger Ribonucleoprotein 1 (FMR1), which encodes an RNA binding protein that is implicated in a multitude of crucial neurodevelopmental processes, including cell specification. We find that zebrafish fmr1 mutants generate surplus ventral lateral descending (VeLD) interneurons, an early-born cell derived from the pMN domain. These GABAergic interneurons are also associated with changes in synaptogenesis, as fmr1 mutants show increased early expression of the scaffold Gephyrin, but these postsynaptic sites fail to mature. Our work shows that Fmrp regulates the proportionate production of neurons that comprise early embryonic motor circuits. As VeLD interneurons are hypothesized to act as central pattern generators driving the earliest spontaneous movements, this imbalance could profoundly influence the formation and long-term function of motor circuits driving locomotion.