Hierarchical sampling from populations, incipient and recognized varie
ties within Phacelia dubia and P. maculata has revealed high levels of
intraspecific polymorphism in chloroplast DNA. Much of the variation
is partitioned between populations as evidenced by population-specific
variants at fixation in all three populations of P. dubia var. interi
or and in both populations of P. maculata. Nine of 16 populations were
polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found
in a sample of 106 individuals; the most common occurred in eight of t
he 16 populations and in 31 per cent of the individuals in the entire
sample. A phylogenetic analysis revealed four basic plastome types. Th
e two major groups of plastomes were separated by four independent bas
e-pair mutations which suggests an ancient split in the evolution of p
lastid genomes. Representatives from each major plastome division were
found in each of five populations spanning two allopatric varieties o
f P. dubia. The geographical distribution of haplotypes and lack of ev
idence for recent admixture argue against migration as a source of the
polymorphism. It is more likely that the current taxonomic varieties
are descendants of a polymorphic common ancestor.