Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went through a moderate bottleneck (approximately 30-40 founders). Linkage disequilibrium was common, both intrachromosomal and between loci on different chromosomes. Of the 15 loci, 2 showed evidence of selection, one exhibiting local adaptation in different populations and the other balancing selection. We conclude that linkage disequilibria may be far more common in natural populations than is generally assumed, and the loci apparently affected by selection may well be marking selection in large genome regions including many loci that are not necessarily closely linked.