The structure of a neural circuit tightly constrains its function. Obtaining synaptic level connectomes is the first step towards understanding their physical implementation. Like any other biological entity, nervous circuits evolved by natural selection, i.e a process of random modification of preexisting structures that become predominant if they confer a reproductive advantage to the individual. Since the modifications have to be compatible with the viability of the organism, “innovations” are constrained and the end product (e.g. brains like ours) result from the accumulation of gradual changes and module repurposing. The comparison of homologous circuits from animals along the tree of life is therefore key to interpret and understand the principles of nervous system organization.To help in this quest, our research aims to generate the fist connectome of Amphioxus lanceolatus, the best studied model organism of the invertebrate to vertebrate transition.