Forty one nuclear probes, distributed across the different linkage gro
ups of the previously published map, were used to examine restriction
fragment length polymorphism between cultivated peppers. Total DNA fro
m thirteen accessions of Capsicum annuum var. annuum and one accession
of C. baccatum var. pendulum was separately cut with ten restriction
enzymes. The analyses were restricted to only one enzyme per probe to
reduce the polymorphism redundancy. Nei & Li's genetic distances betwe
en accessions were calculated from the 141 resultant nuclear DNA restr
iction fragments. The genetic variation was larger between C. annuum a
nd C. baccatum than between C. annuum cultivars. Large fruited related
accessions closely clustered together. Distances between the small fr
uited cultivars were larger than within the bell pepper group. A corre
spondence analysis performed on differences between the global RFLP pa
tterns of each accessions of C. annuum revealed the particular genomic
structure of four small fruited cultivars: Criollo de Morelos 334, H3
, Perennial and Doux Long des Landes. The percentage of probes reveali
ng at least one RFLP with at least one enzyme ranged from zero to fift
y percent for all the pairwise comparisons of C. annuum accessions. 82
presumptive loci were detected with a mean number of 1.46 alleles per
locus within C. annuum and 1.83 within all the accessions. This resul
t indicates that molecular markers will be more usable in intraspecifi
c study of C. annuum than isozyme markers.