A seal structure is provided that follows fluctuations in a gap between a pair of fuel cell separators without generating a large tightening force. A pair of separators facing each other with an electrolyte membrane as a mating member interposed therebetween have beads which form a flow path for fluid between the beads and the electrolyte membrane in close contact with the electrolyte membrane. A seal which seals the pair of separators causes the beads 14 of the pair of these separators to overlap each other in a nested manner. A seal material having elasticity is provided between side walls of the respective beads which face each other. When the gap between the pair of separators fluctuates, the seal material deforms in a shearing direction.