We investigate the generation and decay of interspecific disequilibrium (ID) between organelle and symbiont genomes as a function of the rate of horizontal transmission. We show that rare horizontal transmission greatly diminishes the covariance between organelle and symbiont genomes. This result has two important implications. First, a low level of ID does not indicate low levels of vertical transmission. Second, even with low levels of horizontal transmission, the additive effects of host and symbiont loci will determine the response to selection, while epistatic effects will not be selectable.