Climate change creates complex challenges for smallholder livestock systems in which livestock simultaneously contribute to food production, income, savings, risk management and other household functions. Genetic improvement is increasingly recognised as a component of climate adaptation, with contemporary breeding approaches incorporating environmental heterogeneity, farmer preferences, resilience and changing production conditions. However, climate and socioeconomic change may alter not only the environments in which animals perform but also the configuration of livestock systems themselves through changes in species, breeds, herd or flock structure, enterprise combinations and management. This creates a conceptual problem for future-oriented genetic improvement when the future system for which animals are being improved is itself uncertain. This paper develops a conceptual framework for breeding-objective robustness under future livestock-system uncertainty, drawing together genotype × environment interaction, breeding-objective theory, climate-resilient breeding, community-based breeding, livestock diversification and decision-making under uncertainty. The framework positions future livestock-system configuration and function as an intermediate domain between climate adaptation and genetic-improvement planning. It proposes that where multiple future system configurations are plausible, breeding objectives should be evaluated for robustness across alternative trajectories rather than solely optimised for a single anticipated future. Where uncertainty is deep and alternative objectives diverge substantially, maintaining genetic diversity and the capacity to revise objectives may provide greater strategic flexibility than early narrow commitment. The conceptual contribution is to make uncertainty about future livestock-system configuration an explicit consideration in genetic-improvement planning and to connect this uncertainty with breeding-objective robustness and strategic genetic flexibility.