The alternative oxidase (AOX) is a ubiquinol oxidase with a crucial role in the mitochondrial alternative respiratory pathway, which is associated with various processes in plants. In this study, the activity of AOX in pea seed germination was determined in two pea cultivars, ‘Maravilha d’América’ (MA) and ‘Torta de Quebrar’ (TQ), during a germination trial using cytochrome oxidase (COX) and AOX inhibitors [rotenone (RT) and salicylic hydroxamic acid (SHAM), respectively]. Calorespirometry was used to assess respiratory changes during germination. In both cultivars, SHAM had a greater inhibitory effect on germination than RT, demonstrating the involvement of AOX in germination. Although calorespirometry did not provide direct information on the involvement of the alternative pathway in seed germination, this methodology was valuable for distinguishing cultivars. To gain deeper insights into the role of AOX in seed germination, the AOX gene family was characterized, and the gene expression pattern was evaluated. Three PsAOX members were identified—PsAOX1, PsAOX2a and PsAOX2b—and their expression revealed a marked genotype effect. This study emphasizes the importance of AOX in seed germination, contributing to the understanding of the role of the alternative respiratory pathway in plants.