Understanding the evolution of the bilaterian brain requires a detailed exploration of the precise nature of cellular and subcellular differences between related species. We undertook an electron micrographic reconstruction of the brain of the predatory nematode Pristionchus pacificus and compared the results with the brain of Caenorhabditis elegans, which diverged at least 100 million years ago. We revealed changes in neuronal cell death, neuronal cell position, axodendritic projection patterns, and synaptic connectivity of homologous neurons that display no obvious changes in overall neurite morphology and projection patterns. These multiscale patterns of evolutionary changes show no bias to specific brain regions or neuron types.