Interspecific genetic variation was examined in the genus Capsicum bas
ed on shared restriction fragments in Southern analyses. Four distinct
clusters were delineated among 21 accessions of cultivated and wild p
epper (C. annuum, C. baccatum, C. chacoense, C. chinense, and C. frute
scens). Three tight clusters comprised of accessions belonging to C. a
nnuum, C. frutescens, and C. baccatum, respectively, were formed, alon
g with a fourth cluster comprised of one accession each of C. chinense
and C. chacoense. All accessions were differentiated by this techniqu
e, and the clusters corresponded closely to previous morphology-based
classification. Sufficient DNA polymorphism exists among these accessi
ons that segregating populations useful for restriction fragment lengt
h polymorphism (RFLP) mapping could be constructed using any two peppe
r accessions as parents. Regression analysis indicates that genetic di
stance is a good predictor (R(2) = 0.872) of the level of mappable DNA
polymorphism in Capsicum. Intraspecific variability was examined amon
g four C. annuum cultivars (NuMex R Naky, Jupiter, Perennial, and Crio
llo de Morelos 334) using both RFLPs and randomly amplified polymorphi
c DNA (RAPDs), allowing a comparative evaluation of the two techniques
. Seventeen percent of the clones used singly in RFLP analyses were su
fficient for the differentiation of these varieties, as were 12.5% of
the RAPD PCR amplifications. Dendrograms constructed from RFLP and RAP
D analyses of the intraspecific data are similar but not identical. So
uthern analysis and RAPD PCR should be useful for DNA fingerprinting a
nd the discrimination of closely related C. annuum genotypes.