New methods for the analysis of polymorphisms in DNA sequences have a profound influence on systematic botany. Several recent books deal with molecular methods in evolution and taxonomy (Clegg & O'Brien 1990; Doolittle 1990; Hillis & Moritz 1990; Li & Graur 1991), some of them specifically with plants (Crawford 1990; Soltis et al. 1992). A general revision of the evolutionary relationships of plants with molecular methods seems to be well underway (Palmer et al. 1988). Chloroplast DNA (cpDNA) has turned out to be the most convenient common molecule for the reconstruction of plant phylogeny. In this review, the use of markers in the nuclear genome will be examined. Obtaining reliable phylogenetic information from nuclear DNA tends to be considerably less straightforward than working wth cpDNA. This pertains both to the collection and to the interpretation of the data. However, the features of cpDNA that make it such a useful molecule for phylogenetic analysis also limit its applicability. A brief and simplified comparison of these features with those of nuclear DNA can help point out where and why nuclear markers become important. Chloroplasts contain closed circular DNA molecules about 150 000 base pairs (150 kb) in length. The smallest nuclear genomes in angiosperms are about 500-fold bigger, and the variation in haploid nuclear genome sizes (‘C values’) among the angiosperms is considerable from Arabidopsis thaliana (Brassicaceae) with about 105 kb in the five chromosomes of the haploid genome to Fritillaria assyriaca (Liliaceae) with 1 -23 x 108 kb in 12 chromosomes (Bennett et al. 1982; Price 1988). There can be considerable differences in the genome sizes of closely related congeneric species and there is an increasing number of reports on intraspecific variation in genome size (Price 1991). A variation in C values from 1-84 pg to 7-14 pg (1 pg = 9-5 x 105 kb) among populations of Collinsia verna (Scrophulariaceae) seems to be the widest intraspecific range on record (Greenlee et al. 1984). The range of about 2:1 between the largest and the smallest cpDNA in land plants (Palmer 1985) is small in comparison and easy to explain. The availability of the complete sequences of several cpDNAs facilitates considerably the evolutionary comparison (Ohyamacta/. 1986; Shinozaki et al. 1986).