For neutral genes, uniparental inheritance is expected to reduce effective population size relative to biparentally inherited genes. In finite populations, the ensuing genetic drift can cause stronger spatial and temporal differentiation. An intrapopulation polymorphism in chloroplast DNA was used to examine relative spatial and temporal population structure of chloroplast and allozyme markers in the annual plant Phacelia dubia. There was significant differentiation among populations at chloroplast markers but not for allozyme loci. A fine-scale analysis showed significant structure among sites within populations for chloroplast markers and local heterozygote deficiencies at allozyme loci. These spatial analyses suggest that gene flow via pollen exceeds that via seed. Temporal variation in chloroplast markers, assessed over a 10-year period, was evident in two of four populations, and allozyme loci were characterized by temporal variation in rare-allele frequencies. Population structure appeared to be related to the intensity and type of human disturbance influencing each population. Habitat destruction promoted isolation and enhanced differentiation, whereas mowing increased seed dispersal and reduced differentiation for chloroplast markers. At this time, genetic drift appears to be the primary force shaping chloroplast gene frequencies.