Understanding the variation within and between populations in important male mating traits and female preferences is crucial to theories concerning the origin of sexual isolation by coevolution or other processes. There have been surprisingly few studies on the extent of variation and covariation within and between populations, especially where the evolutionary relationships between populations are understood. Here we examine variation in female preferences and a sexually selected male song trait, the carrier frequency of the song, within and between populations from different phylogeographic clusters of Drosophila montana. Song is obligatory for successful mating in this species, and both playback and field studies implicate song carrier frequency as the most important parameter in male song. Carrier frequency varied among three recently collected populations from Oulanka (Finland), Vancouver (Canada), and Colorado (central United States), which represent the main phylogeographic groups in D. montana. Males from Colorado had the most distinct song frequency, which did not follow patterns of genetic differentiation. There was considerable variation in preference functions within, and some variation between, populations. Surprisingly, females from three lines from Colorado seem to have preferences disfavoring the extreme male trait found in this population. We discuss sources of selection on male song and female preference.