The assembly of functional neural circuits relies on the generation of diverse neural types with precise molecular identity and connectivity. Unlocking general principles of neuronal specification and wiring across the nervous system requires a systematic and high-resolution characterisation of its diversity, recently enabled by advances in single-cell transcriptomics and connectomics. However, linking the molecular identity of neurons to circuit architecture remains a key challenge. Here, we present a high-resolution developmental transcriptional atlas for the Drosophila melanogaster nerve cord, the central hub for sensory-motor circuits. With an unprecedented 38x coverage relative to its reference connectome1,2, our atlas captures extensive molecular diversity and enables robust alignment to the adult connectome. We identified three developmental principles underlying neuronal diversity in the nerve cord. First, timing of neurogenesis shapes molecular identity: embryonic-born neurons adopt discrete molecular identities, while larval-born neurons form continuous identities within lineages, a distinction we also found in the adult connectome. Second, we discovered that the continuous molecular progression is mirrored by the expression dynamics of 17 transcription factors. These factors are common to neurons from all lineages and provide a global molecular identity code based on birth order. Lastly, by mapping sex-specific transcriptional profiles to the connectome, we uncovered female-specific apoptosis and transcriptional divergence as key global drivers of sex-specification. By revealing key organisational axes of molecular identity, this atlas opens new avenues to dissect the molecular mechanisms underpinning the development and evolution of neural circuits.