We assessed the variation in thorax size, wing size and wing loading in populations of Drosophila subobscura from two ecologically different habitats and within each habitat sampled during three periods of the day. The traits analyzed differed between laboratory reared samples and field collected samples. Differences were mainly caused by environmental factors and genotype x environmental interactions. While there were no significant differences between populations for particular periods of the day, within-population analysis for each sex showed specific differences. Results showed that wing loading was the least variable character in natural populations, also showing the lowest level of sexual dimorphism. The data are discussed from the aspect of the variability of gene arrangement frequencies over daytime periods obtained previously for the same samples. They are consistent with models of maintenance of genetic variability in multi-niche habitats, and are in favour of a type of reactive behaviour dependent on ecological niche qualities on a daily rhythm scale in D. subobscura.