Analysis of contemporary evolution can provide important insights into the pattern and rate of phenotypic evolution. The threespine stickleback population in Loberg Lake was exterminated in 1982, and a new population was founded between 1983 and 1989 by anadromous stickleback. The body shape of the Loberg Lake population resembled that of anadromous populations in 1990, although it had diverged markedly by 1992. Between 1992 and 2009, the population evolved more slowly to resemble typical lake populations in the region, diverging approximately 68% of the distance separating its putative ancestor and the original native population by 2009. Temporal evolution is the main source of variation, although spatial heterogeneity, armour phenotype, and allometry contribute significant variation. There was no significant effect of ancestral phenotypic shape covariance on the evolutionary trajectory of this population. Temporal variation in the Loberg Lake population provides a rare glimpse into the evolutionary response of a complex trait to natural selection after a major habitat shift. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 817–831.