Self-assembly of spin-labeled synthetic macromolecules or biomacromolecules can lead to structures that contain more than two nitroxide radicals. Label-to-label distance distributions are then poorly resolved since established electron paramagnetic resonance techniques for distance measurements cannot select between the different pairs of nitroxides. A separation into different contributions can be achieved by partially labeling the nitroxide radicals by (15)N or by deuterium and applying pulse electron electron double resonance techniques. With (15)N labeling, strong suppression of either the (14)N or the (15)N contribution can be achieved by suitable choices of the excitation bandwidths and frequencies of the observer subsequence and pump pulse and linear combination of data sets. With deuterium labeling, interactions between only the isotope-labeled nitroxides can be selected by a two-dimensional version of the four-pulse double electron electron resonance experiment. This selection is based on the deep electron spin echo envelope modulation of deuterated nitroxides.