Tools allowing to understand the evolution of donkey populations in time, the future trends that these populations describe, and the factors conditioning such trends, become invaluably critical when aiming at preserving and later recovering such populations from their endangerment status. Basing on the characteristic lack of information regarding the genealogical background of donkey populations and taking a particular breed as an example, it is possible to infer a model to assess the genetic and demographical structure of other international endangered donkey populations. Then, we can plot selection strategies to implement once such populations have reached the sufficient number of individuals, and are supported by solid enough structures. Microsatellite-tested pedigree analyses were carried out to study the genetic diversity, structure and historical evolution of the Andalusian donkey breed since the 1980s. Despite mean inbreeding was low, highly inbred animals were present. The effective population size based on individual inbreeding rate was about half when based on individual coancestry rate. Nei's distances and equivalent subpopulations number indicated differentiated farms in a highly structured population. Although genetic diversity loss since the founder generations could be considered small, intraherd breeding policies and the excessive contribution of few ancestors to the gene pool could lead to narrower pedigree bottlenecks. Long average generation intervals could be considered when reducing inbreeding. Wright's fixation statistics indicated slight inbreeding between farms. Pedigree shallowness suggested applying new breeding strategies to reliably estimate descriptive parameters and control the negative effects of inbreeding, which could indeed, mean the key to preserve such valuable animal resources avoiding the extinction they potentially head towards. Diversity studies render especially important in donkeys as they reveal the genetic background in the populations and the starting point for making decisions on whether to apply conservation or breeding plans in this functionally misallocated species. Once genetic diversity parameters are balanced, finding new niches for donkeys becomes potentially the most relevant aim to approach in the midterm future for the species. Selection strategies in donkeys are approached from three different perspectives; donkey-assisted therapy and therapeutic riding, fertility and disease resistance, not only as a way to widen the functional spectrum of opportunities of donkeys but also to lengthen their useful lives, and improve their life quality and welfare. Studying the specific genetic background behind functional traits enables quantifying the degree in which such features pass from jacks and jennies onto the new foal generations. As a genetic term, environment means all influences other than inherited factors. Controlling the environmental factors conditioning the expression of certain functional features help to build animal models shedding light in the genetic fraction involved in such functional traits. The functional performance of 300 microsatellite-assisted parentage tested donkeys was studied using REML and Gibbs sampling Bayesian methods for the obtention of genetic parameters and breeding values using BLUP methodology. The first functional niche for which donkeys may be well-suited is linked to their special psychological nature and physical characteristics as facilitators of learning processes and for the development of key life skills and confidence building for a wide spectrum of vulnerable people. Therapeutic riding and asinotherapy take advantage of the physical and psychological interaction between donkeys and patients given the potential application of donkey's characteristics and abilities for the treatment of specific human disorders. The selection of donkeys when the breeding criteria is their suitability for equine-assisted therapies was implemented following two different approaches; the selection for coping styles and cognitive processes and the selection for gaits and kinetics. Aiming at developing suitable models seeking the consolidation of equine assisted-therapy breeding criteria, we studied 29 factors that may potentially influence several cognitive processes in donkeys. These factors not only affect donkeys' short-term behaviour but may also determine their long-term cognitive skills from birth. Thus, animal behaviour becomes a useful tool to obtain past, present or predict information from the situation of a certain animal in a particular area. Operant conditioning and Qualitative Behavioural Assessment (QBA) synergism can provide valuable information about animals' extinction/learning and emotional status. All noncognitive animal inherent features significantly affected four variables (P<0.001), although some were not linearly correlated. On the other hand, the effect power of meteorological factors ranged from 7.9% for the birth season on learning (P<0.05) to 38.8% for birth moon phase on mood (P<0.001). Psychometric testing enables quantifying animal cognitive capabilities and their genetic background. Among these cognitive capabilities, the study of problem-solving coping styles achieves a special relevance as it brings together the need genetically select donkeys displaying a neutral reaction during training, given its implication with handler/rider safety and trainability. Heritabilities for coping style traits were moderate, 0.18 to 0.21. Phenotypic correlations between intensity and mood/emotion or response type were -0.21 and -0.25, respectively. Genetic correlations between the same variables were -0.46 and -0.53, respectively. Phenotypic and genetic correlations between mood/emotion and response type were 0.92 and 0.95, respectively. Principal components and Bayesian analyses were used to compute the variation in cognitive capabilities explained by 13 cognitive processes and their genetic parameters, respectively. Heritabilities ranged 0.06 to 0.38 suggesting the same patterns previously reported for humans and other animal species. By contrast, when considering the selection for therapeutic riding, gaits' heritability estimates ranged from 0.53 to 0.67 for walk and trot, respectively. Genetic correlations ranged from 0.28 to 0.42, for walk/trot and amble/trot, respectively. Our results suggest that gait genetic lines could be developed. Among other breeding criteria, disease resistance and reproduction offer two functional niches to consider given their relationship with donkey life quality and welfare. Breeding programs selecting for disease resistance could address food safety and quality issues in products such as donkey milk, and may be perceived to be more humane. Cutaneous habronematidosis (CH) is a highly prevalent parasitic seasonally recurrent skin disease causes distress and relapsing wounds to the animals. CH hypersensibility heritability was 0.0346. Genetic parameters and breeding values for functional traits enable planning strategies for endangered donkey breed preservation and breeding what may turn into a measure to improve animal welfare indirectly.Multiple births in equids are dangerous situations that compromise the life of the dam and offspring. However, embryo collection techniques take advantage of individuals whose multiple ovulations allow flushing more fertilized embryos from the oviduct. Heritabilities ranged from 0.18 to 0.24. Genetic and phenotypic correlations ranged from 0.496 to 0.846 and 0.206 to 0.607, respectively.