Genotypic diversity in six populations of the endemic Hawaiian reef co
ral, Porites compressa, was directly related to habitat-disturbance hi
story. The highest diversity (lowest amount of clonal proliferation) w
as found in populations that had been intensely or recently disturbed.
In these populations, space was not limited and mean colony size was
small (< 500 cm(2)), suggesting early stages of recolonization. In an
undisturbed, protected habitat, lower genotypic diversity was a result
of a significant degree of clonal replication of established genotype
s. Unoccupied substratum was rare in this habitat, and average colony
size was large (> 2500 cm(2)). Populations in intermediately disturbed
habitats showed intermediate levels of diversity and clonal structure
as a result of the combined contributions of sexual and asexual repro
duction. Individual clones were distributed over small areas (< 4 m(2)
) or distances (< 1 m) in young populations, and more broadly (> 256 m
(2)) and over longer distances (> 90 m) in the older, undisturbed popu
lation. Interpretations of life-history parameters and estimates of to
tal genetic variability in species that have the potential to reproduc
e asexually are dependent upon an assessment of the overall clonal str
ucture of populations. The power of genotypic assays to reliably detec
t clonal versus unique colonies, as well as the spatial scales over wh
ich clonal populations are sampled, are critical to such assessments.