The invention concerns a method for identifying cognate pairs of a ligand species and a receptor species, comprising co-compartmentalising ligand species and receptor species to form a set of microreactors, each microreactor comprising at least one ligand species and preferably at least one receptor species; assaying the recognition between ligands and receptors in each microreactor and based on this assay, classifying each microreactor as positive when at least one ligand species and at least one receptor species in the microreactor recognize one with the other or negative when no ligand species and no receptor species recognize in the microreactor; identifying ligand species and receptor species contained in each positive microreactor; establishing a subset of positive microreactors containing the same receptor species; determining the probability that in a given subset of positive microreactors containing the same receptor species, the ligand species recognizing the receptor species corresponds to the most frequent co-compartmentalized ligand species; and if the determined probability is greater than a predetermined threshold, identifying as a cognate pair the receptor species and the most frequent co-compartmentalized ligand species.