AbstractRhizobium melilotistrains isolated from alfalfa plants grown in a mining recultivation field, in a model ecosystem (microcosm) and in soil core containers were characterized by two new taxonomic methods, fingerprinting and handprinting, using insertion sequence elements (IS) as hybridization probes. The diversity of strains within the field population could first be detected with IS‐fingerprinting, whereby nearly three times more groups ofRhizobium melilotistrains could be identified in comparison to the groups according to plasmid profiles. This complexity and diversity of the rhizobial population was also detected in microcosm studies. Strains identified among the field population were also detected in the microcosm studies. The persistence of rhizobia in soil was demonstrated in soil core samples held in a cold room for 2 years. A decrease in the genomic diversity of the R.melilotipopulation upon soil storage was observed. A novel monitoring method, IS‐handprinting, in which the presence of certain endogenous insertion elements within a strain is registered, was successfully employed to characterize genetically the fieldR. melilotistrains with simplicity and speed. In contrast to IS‐fingerprinting, IS‐handprinting is based on a simple plus‐or‐minus detection, which is sufficient for a taxonomic characterization. Both methods, using a non‐radioactive detection system, are sensitive enough to detect one copy of an insertion element in a strain's genome. IS‐fingerprinting, with its fine resolution, would be suitable for ecological studies of individual strains in any complex ecosystem, whereas IS‐handprinting would be suitable for monitoring strains and characterizing large n