Root-knot nematodes (genus Meloidogyne) have been the subject of recen
t and numerous studies of genetic variation because of the need to dev
elop molecular diagnostics for the four globally distributed, partheno
genetic species that are significant agricultural pests. Our analysis
of Meloidogyne mtDNA improves on previous studies: (i) by examining re
striction site polymorphism among a large number of isolates also char
acterized for standard morphological, host range and allozyme phenotyp
es; (ii) by using higher resolution electrophoretic techniques; and (i
ii) by mapping variable restriction sites with reference to the comple
te nucleotide sequence. This revealed fivefold less sequence divergenc
e (<0.6%) between variants than estimated in previous restriction frag
ment length polymorphism (RFLP) studies, but perfect correspondence be
tween mtDNA haplotype and allozyme (esterase) phenotypes pes. The mtDN
A variation, although limited, is strongly structured with as much div
ergence between two lineages of Meloidogyne arenaria as between either
of these and Meloidogyne javanica. The low diversity of mtDNAs sugges
ts that these parthenogenetic lineages arose from distinct but closely
related sexual females, a pattern seen in other parthenogenetic compl
exes. In contrast to the concordance between mtDNA and allozyme marker
s, there were several discrepancies between the traditional methods of
identification. We suggest that further studies of these nematodes sh
ould focus on well defined genetic groups, whether or not these coinci
de with existing taxonomic units.