Introduction The Pampas deer (Ozotoceros bezoarticus L. 1758) is the most endangered neotropical cervid. Although it has a wide geographical distribution in south-eastern South America (from 5° to 41° S), the habitat required by this species has been greatly reduced by agriculture and urbanization. The Pampas deer formerly occupied a range of open habitats such as grassland, pampas, savanna, and cerrado (Brazil). However, the area encompassed by these habitats has been dramatically reduced to less than 1% of that present in 1900 (González 1993, 1996). Currently, Pampas deer populations are generally small and highly isolated (Jackson & Langguth 1987; González 1993; Merino 1994; Pinder 1994; Fig. 1). The largest extant populations are found in Brazil, in the north-east cerrado ecosystem where about 2000 individuals live, and in the Pantanal where 20 000–40 000 exist (Pinder 1994). In Uruguay there are two main populations: El Tapado (Salto Department) with about 800 individuals, and Los Ajos (Rocha Department) with about 200 deer (González 1996). At the turn of the century, the Argentinean population was prob- ably very large as over 500 000 km 2 of grassland habitat was available. However, today only three small popula- tions remain: Corrientes (Ituzaingo Department) with about 170 individuals (ML Merino & MD Beccaceci, Conservation genetics of the endangered Pampas deer (Ozotoceros bezoarticus) S. GONZÁLEZ,* J. E. MALDONADO,† J. A. LEONARD,† C. VILÀ,† J. M. BARBANTI DUARTE,‡ M. MERINO,§ N. BRUM-ZORRILLA* and R. K. WAYNE† *División Citogenética, IIBCE, Av. Italia 3318, Montevideo, 11600 Uruguay; †Department of Biology, 621 Circle Drive South, University of California, Los Angeles, CA 90095–1606, USA; ‡Departamento Melhoramento Genético Animal, FCAVJ/UNESP, Rod. Carlos Tonanni km 5, 14870–000 Jaboticabal, SP, Brazil; §Estación de Cría de Animales Silvestres, CC 129, Villa Elisa, Buenos Aires, Argentina Abstract The Pampas deer (Ozotoceros bezoarticus L. 1758) is the most endangered neotropical cervid, and in the past occupied a wide range of open habitats including grassland, pampas, savanna, and cerrado (Brazil) from 5° to 41° S. To better understand the effect of habitat fragmentation on gene flow and genetic variation, and to uncover genetic units for conservation, we examined DNA sequences from the mitochondrial control region of 54 individuals from six localities distributed throughout the present geographical range of the Pampas deer. Our results suggest that the control region of the Pampas deer is one of the most polymorphic of any mammal. This remarkably high variability probably reflects large historic population sizes of millions of individuals in contrast to numbers of fewer than 80 000 today. Gene flow between populations is generally close to one migrant per generation and, with the exception of two populations from Argentina, all populations are significantly differentiated. The degree of gene flow was correlated with geographical distance between populations, a result consistent with limited dispersal being the prim- ary determinant of genetic differentiation between populations. The molecular genetic results provide a mandate for habitat restoration and reintroduction of Pampas deer so that levels of genetic variation can be preserved and historic patterns of abundance can be reconstructed. However, the source of individuals for reintroduction generally should be from populations geographically closest to those now in danger of extinction. Keywords: Cervidae, conservation, control region, mitochondrial DNA, Ozotoceros bezoarticus, phylogeography Received 20 March 1997; revision received 1 August 1997; accepted 2 August 1997 Molecular Ecology (1998) 7, 47–56 © 1998 Blackwell Science Ltd Correspondence: R. K. Wayne, Tel.: +1-310-206-0334; Fax: +1-310- 206-3987; E-mail: rwayne@biology.ucla.edu