The 1990–2002 era saw neurogenomics integrate genome-wide resources with developmental neurobiology, enabling systematic gene discovery, functional annotation, and cross-species comparisons of neural pathways. Genome sequencing and functional genomics frameworks accelerated mapping of neural gene networks and neurotrophic signaling, aligning molecular genetics with neuroscience. Notable milestones include the nematode genome sequence providing a platform for functional genomics and comparative neural studies, the expansion of the neurotrophin family with Neurotrophin-3 as a critical factor for neuronal survival and differentiation, the identification of the Type 1 Neurofibromatosis gene linking neural development signaling to tumor predisposition and personalized medicine, and the discovery of neurogenin1 as a key transcriptional regulator of neuronal precursor fate in cranial sensory development. Historical Significance: These advances defined a genome-informed paradigm for decoding neural development and disease, weaving together genetics, molecular biology, and neuroscience. They established foundational models for regulatory networks and trophic signaling, enabling systems-level approaches and informing later high-throughput sequencing, computational biology, and precision neuromedicine. The period's integrative perspective unified developmental neurobiology with genomic science, setting the stage for rapid progress in neurogenomics throughout the 2000s.