The technique of DNA fingerprinting is frequently used for studies of genetic diversity and relatedness in a wide range of organisms. In humans and animals, multilocus fingerprints are mainly applied to paternity and identity test cases, behavioral ecology, and the analysis of population structures. In plants and fungi, the frequent occurrence of "low-variability" fingerprint patterns additionally allows to use multilocus fingerprinting for studying taxonomical problems at an intraspecific level. In the present article, we (1) present an overview of such approaches in a series of plant species, (2) summarize our attempts to estimate genetic relationships within two cultivated plant species, banana and tomato, by band sharing data derived from oligonucleotide fingerprints, and (3) discuss the limitations and potentials of multilocus fingerprinting for the determination of genetic relatedness.