With ca. 100,000 total neurons and less than 20,000 neurons per central brain hemisphere (excluding the lower visual processing centers), the fruit fly Drosophila melanogaster provides a feasible target for analyzing all the neurons and their network in the whole brain. Light microscopy approach by visualizing various neuron types with the ectopic expression of reporter proteins has the resolution limit of light wavelength. But it enables single-neuron labeling of individual transmitter types and complete tracing of long-range axons as well as fine branches. Electron microscopy approach by segmenting the whole-brain serial section images can analyze only one brain sample, and complete tracing of entire neurites is difficult. But it enables high-resolution identification of input/output synapses to map the comprehensive neuronal connectivity. Our recent research, e.g., the identification and classification of over 4,000 novel neuron types based on the whole brain electron microscopy data by HHMI Janelia Research Campus, complete identification of monoaminergic neurons with light microscopy labeling and the identification of matching neurons in the electron microscopy data as well as their connectome analysis, and the classification of long-rage somatosensory ascending neurons from the nerve cord to the brain, will be introduced.