The genetic heterogeneity of two M. arenaria race 2 populations (desig
nated Pelion and Govan) was examined using RFLP analysis of 12 clonal
lines established from single egg masses (six distinct clonal lines fr
om each population). These populations are essentially identical by tr
aditional biochemical and race identification schemes; however, the Go
van population is more aggressive than the Pelion population, producin
g larger galls and exhibiting greater reproductive capabilities on man
y soybean cultivars and experimental accessions. Variation at the geno
mic DNA level was examined using probes representative of expressed DN
A sequences present in the eukaryotic genome. Ribosomal DNA, intersper
sed repeated sequences, and cDNA probes were tested for detection of p
olymorphism within and between single egg mass lines of each populatio
n. Cloned cDNAs and ribosomal intergenic spacer sequences detect polym
orphism both within and between populations, demonstrating the usefuln
ess of these sequence classes for molecular genetic analysis of popula
tion structure and genome evolution.