It is beginning to be possible to test for the action of natural selection in nonmodel species, including in natural populations of plants, using DNA sequence diversity within species and divergence between related species. We suggest some questions of interest in plants in the genus Silene, where the evolution of unisexuals has occurred multiple times and related species suitable for use as outgroups in such comparisons are available. In the dioecious species Silene latifolia, the evolution of separate sexes raises many questions about selection, including the possibility of recent selective sweeps on the Y or other chromosomes. If recent selective sweeps have not occurred on the Y chromosome, one might be able to conclude that the low sequence diversity that is observed for Y-linked genes may be due to processes involved in genetic degeneration of Y chromosomes. In a dioecious species, it is also interesting to test whether sexual selection occurs (a question that has been difficult to study in plants and which could affect the effective population sizes of genes on the X and Y chromosomes and on the autosomes, which must be taken into account when testing for selection), and also whether selection occurs during pollination. Silene latifolia is also useful for testing selection in other Silene species, and we outline tests for long-term balancing selection in the mitochondrial genome associated with the presence of females in the gynodioecious species Silene vulgaris. The results of our tests for selection are preliminary, and there are important caveats associated with the conclusions. We therefore include discussion of some of the main difficulties and the kinds of data that should be helpful in refining the results in the future.