The recognition of three genera of living zapodines (Ellerman, 1940; Klingener, 1963; Krutzsch, 1954; R. A. Martin, 1994), which we retain here, has been challenged by Corbet (1978c), Corbet and Hill (1992), and Simpson (1945), who included Eozapus in Zapus. Higher level relationships among zapodines have been addressed by Preble (1899), who described Eozapus and Napaeozapus as new subgenera of Zapus, and by Krutzsch (1954), who supported generic separation based on differences in tooth number and occlusal pattern, bacula, and ear ossicles. Klingener (1964:75) found no consistant differences in the myology of Zapus versus Napaeozapus (Eozapus was not included in his study), but favored generic separation of the two based on dental morphology. The dental differences between Eozapus on one hand, and Zapus and Napaeozapus on the other, as documented in Klingener (1963), R. A. Martin (1994), Preble (1899), van de Weerd (1976), and Krutzsch (1954), are particularly striking and phylogenetically significant (e. g., "dental features of Eozapus . . . are completely different from those of . . . Zapus and Napaeozapus," van de Weerd, 1976:139). Molar occlusal patterns and degree of hypsodonty in Eozapus, especially the lowers, are primitive and closely resemble molar structure in the extinct sicistine Plesiosminthus (late Oligocene to Miocene in North America and Eurasia); those of Zapus and Napaeozapus are highly derived (Klingener, 1963; R. A. Martin, 1994). External traits of Eozapus, by contrast, closely resemble Napaeozapus and Zapus in pelage color and pattern and in saltatory adaptations (elongate hind legs and feet, long tail relative to body length) characterizing the other two genera, and possibly "the appearance of the first zapodine dentition in the fossil record also signals the first filling of the jumping mouse adaptive zone" (R. A. Martin, 1994:105).

Evolutionary history of zapodines, as documented by fossils, extends back to early Miocene of Kazakhstan and Mongolia, late Miocene in North America, Europe, and China, and is represented by species in the three recent genera and the extinct Asiazapus, Javazapus, Pliozapus, Sinozapus, and Sminthozapus (Fahlbusch, 1992; Lopatin and Zazhigin, 2000; Qiu and Storch, 2000; R. A. Martin, 1994). Judged by fossil evidence, zapodines may have originated in Asia with Eozapus prosimilis (early Miocene of Mongolia) basal to Eurasian species, and Asiazapus (late Miocene of Kazakhstan) closely related to North American Zapus and Napaeozapus (Lopatin and Zazhigin, 2000).