A seal structure for an electronic control device having a circuit board housed in a watertight space a housing that is formed by fitting a plurality of fitting members together, has first and second seal portions which are formed at a fitting surface portion between the fitting members that are fitted together. One side of a pair of the fitting members of each of the first and second seal portions is provided with a seal groove, the other side is provided with a protruding line. An auxiliary seal groove and an auxiliary protruding line are formed on opposing surfaces of the seal groove and the protruding line at a merged part where the first and second seal portions meet each other. The auxiliary seal groove and the auxiliary protruding line continuously extend from the seal groove up to an end surface of the protruding line.