The proteins responsible for mitochondrial function are encoded by two different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual lineages provide a powerful means of addressing these challenges by enabling comparisons among genetically identical individuals in which nuclear and mitochondrial genomes are co-inherited. Here, we used Potamopyrgus antipodarum, a New Zealand freshwater snail that is an emerging model system for the evolution of sexual reproduction, adapting several methods for measuring mitochondrial function in mollusks at three distinct levels of biological organization: mitogenomic, organellar, and organismal. We applied these methods to multiple asexual lineages of P. antipodarum and evaluated whether there exists genetic variation (that is, the raw material for adaptive evolution) for mitochondrial genome copy number, mitochondrial membrane potential, and organismal oxygen consumption. Our analyses revealed that asexual lineages of P. antipodarum differed in terms of mitochondrial function at all three levels of biological organization. The discovery of lineage-level variation in terms of mitochondrial function combined with the methods developed here set the stage to study central evolutionary questions including whether mitochondrial mutation accumulation influences the maintenance of sexual reproduction in natural populations.