Molecular methods which identify species-specific genetic markers are valuable for identification and genetic analysis of hybrid deer. We have used a variety of molecular techniques to compare Père David's deer Elaphurus davidianus, red deer Cervus elaphus scotticus and North American wapiti C. e. manatobensis. In total, these analyses have identifed over 300 markers in which Père David's deer sires are distinct from farmed red deer and over 100 markers in which wapiti sires differ from red deer. Subsets of these markers have been used to identify hybrids on farms, and to estimate the proportion of red deer and wapiti in hybrid animals. Analysis of the segregation of the species-specific alleles in 352 backcross 1/4 Père David's, 3/4 red deer hybrids has produced a deer genetic linkage map which describes the chromosomal grouping and order of the markers. Correlation of the variability in phenotypic traits with marker segregation in the back-cross hybrids has located genes which influence variation in gestation length, pedicle-initiation, birth weight, growth rate and a variety of morphological traits in Père David's deer x red deer hybrids. Such genetic analyses can now be extended, using new marker technologies, to more closely related taxa, such as farmed red deer and wapiti hybrids, and potentially analyse natural hybrid zones.