A bonding apparatus includes a bonding stage on which either a rectangular substrate or a circular substrate can be installed; a first transport mechanism which transports the rectangular substrate from a first carry-in unit to the bonding stage and from the bonding stage to a first carry-out unit; and a second transport mechanism which transports the circular substrate from a second carry-in/out unit to the bonding stage and from the bonding stage to the second carry-in/out unit, in which a first transport path determined by the first transport mechanism and a second transport path determined by the second transport mechanism partially overlap.