Fault tolerance may be achieved in a branched optical communication system such that a fault in one optical path may not affect optical signals coupled from a healthy optical path. In general, a flexible branching unit is configured, when adding and dropping channels, to select channels from a healthy path and not from the faulty path (e.g., a trunk path or a branch path) to prevent non-uniform channel loading on the trunk path after the branching unit. In this manner, a fault detected on the trunk path may not affect signals from the branch path and a fault detected on the branch path may not affect signals from the trunk path, thereby providing fault tolerance. A flexible branching unit may also be capable of adjusting the number and selection of channels that are added and dropped at the branching unit.