We establish a Lie theory for singular subalgebroids, objects which generalize singular foliations to the setting of Lie algebroids. First we carry out the longitudinal version of the theory. For the global one, a guiding example is provided by the holonomy groupoid, which carries a natural diffeological structure in the sense of Souriau. We single out a class of diffeological groupoids satisfying specific properties and introduce a differentiation-integration process under which they correspond to singular subalgebroids. In the regular case, we compare our procedure to the usual integration by Lie groupoids. We also specify the diffeological properties which distinguish the holonomy groupoid from the graph.