We investigate the dynamics of model microswimmers under confinement, in cylindrical geometries, by means of three dimensional direct numerical calculations with fully resolved hydrodynamics. Such swimmers are known to show collective alignment in bulk, and we confirmed that similar alignment can be observed even in pipes, although the volume fraction dependency shows qualitative differences. By comparing the structural information, we investigated the cause of such differences. We found an order/disorder phase transition for a specific type of swimmers, as the size of the pipe becomes comparable to the size of the swimmers. Such dynamics are found not to depend on the geometry of confinement.