Selection on mitochondrial mutations potentially occurs at different levels: at the mitochondria, cell, and organism levels. Several factors affect the strength of selection at these different levels; in particular, mitochondrial bottlenecks during germline development and reduced paternal transmission decrease the genetic variance within cells, while they increase the variance between cells and between organisms, thus decreasing the strength of selection within cells and increasing the strength of selection between cells and organisms. However, bottlenecks and paternal transmission also affect the effective mitochondrial population size, thus affecting genetic drift. In this article, we use a simple model of a unicellular life cycle to investigate the effects of bottlenecks and paternal transmission on the probability of fixation of mitochondrial mutants and their frequency at mutation-selection equilibrium. We find that bottlenecks and reduced paternal transmission decrease the mean frequency of alleles with s m Ͼ s c (approximately), where s m and s c are the strengths of selection for an allele within and between cells, respectively, and increase the frequency of alleles with s m Ͻ s c . Effects on fixation probabilities are different; for example, bottlenecks reduce the fixation probability of mutants with s m Ͼ 0 (unless s m is very small relative to s c ) and increase the fixation probability of mutants with s m Ͻ 0.