Genetic subdivision of a species indicates the potential for local adaptation, and the genetic differences among populations are a key component of genetic diversity. Molecular genetic markers are generally used to assess the extent and pattern of subdivision. These traits provide an abundance of simple genetic markers, and they allow comparisons across studies. However, the connection of molecular genetic variation to local adaptation and, hence, to possible genetic problems of translocation, is weak. In the extreme case of no genetic subdivision, there is no reason to expect genetic problems with translocation. Where there is deep genetic structure, indicating substantial evolutionary independence of sets of populations, translocations may threaten basic components of genetic diversity. Between these extremes, however, predicting genetic problems of translocations is extremely difficult. The molecular markers used to measure genetic structure indicate where there has been opportunity for local adaptation, but they are not directly related to such adaptation. The relationship of the level of genetic divergence to genetic incompatibilities is very loose, although quantitative tests are scarce. However, studies of reproductive isolation between species illustrate the fundamental inadequacy of using measures of genetic divergence to predict interactions between populations. Although it is tempting to use simple measures as predictors, such use may provide a false sense of scientific rigour. There is no substitute for direct tests for variation in ecologically relevant traits and possible genetic incompatibilities among populations.