A control system for spectral slot assignment in flexible grid optical networks determines, for a given optical path, a physical source node, a physical destination node, and physical intermediate nodes, determines the number of contiguous spectral slots to allocate for traffic on the path, identifies candidate combinations of spectral slots available for the traffic, and creates an auxiliary graph for the path. The auxiliary graph includes auxiliary links representing candidate combinations of spectral slots, virtual nodes representing pairs of neighboring physical nodes, and auxiliary links between each pair of virtual source-side and destination-side intermediate nodes representing either pass-through traffic or wavelength shifted traffic. The control system assigns cost values to the auxiliary links, determines a lowest cost combination of auxiliary links from the source to the destination, allocates the corresponding candidate combinations of spectral slots to the traffic, and configures the physical intermediate nodes accordingly.