The effect of selection on the amounts of nucleotide variation within and between allelic classes was studied when two allelic classes exist in a population. Two selection models – the genic selection model and the overdominant selection model – were used. The average numbers of pairwise nucleotide differences within two allelic classes were investigated by computer simulation and the average number of pairwise differences between two allelic classes was obtained analytically. It was indicated that selection largely affects the amounts of variation within and between allelic classes. However, the sum of the average numbers of pairwise differences within two allelic classes is nearly constant and always close to θ(θ=4Nμ), even when selection is acting, where N is the effective population size and μ is the mutation rate per sequence per generation. This result suggests that the sum of the average numbers of pairwise differences within two allelic classes can be used to estimate θ. It may be useful for a region where selection may be acting. As examples, several gene regions of Drosophila melanogaster and a region of Mus domesticus were analysed. The effect of recombination on the sum of the average numbers of pairwise differences within two allelic classes was discussed.