In a study of the widespread Australian endemic seagrass Posidonia aus
tralis, allozyme analysis identified a wide range in population geneti
c structure assessed using the multilocus genotype diversity statistic
(DG). Values of DG between zero and one were obtained; however, RAPD
analysis generally detected higher levels of diversity, where DG value
s were all greater than 0.5 (D-G = 0.67 - 1). Some populations were al
lozymically monomorphic using allozyme analysis yet were highly polymo
rphic using RAPD analysis. The differences observed between methods, p
articularly among allozymically uniform populations, demonstrate the i
mportance of choosing an appropriate method when assessing genotypic d
iversity. Different methods may reflect different historical aspects o
f population processes where allozymes reflect broader-scale gene flow
and population establishment and DNA fingerprinting methods such as R
APDs may reflect fine-scale local recruitment events and shorter-term
population processes. Using either method alone, particularly in genot
ypically depauperate organisms such as seagrasses and other clonal org
anisms, will be problematic in assessing their population genetic pote
ntial, a parameter being used by conservation managers to decide upon
management strategies in rare and endangered organisms. It is recommen
ded that the impact of disturbance assessed using genotypic diversity
measures requires more than one technique to provide the most appropri
ate information for designing subsequent conservation strategies.