An alignment apparatus for a substrate bonding system is provided with a first optical arm arranged to direct onto a detector radiation from a first alignment mark on a first substrate, and a second optical arm arranged to direct onto the detector radiation from a second alignment mark on a second substrate. The first alignment mark has a known location relative to a functional pattern provided on an opposite side of the first substrate, and the second alignment mark has a known location relative to a functional pattern provided on an opposite side of the second substrate. The substrate bonding system can be further provided with first and second substrate tables arranged to hold the first and second substrates such that they face one another, at least one of the substrate tables being movable in response to a signal output from the detector, thereby allowing the first and second substrates to be aligned with respect to each other for bonding.