Most of the attention given to intraspecific crop, livestock, and aquaculture diversity in agricultural production systems has been targeted at their roles in providing provisioning services, such as food and fibre or their cultural services, providing non-material benefits, such as places for recreation and inspiration. The additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services for agricultural productivity and ecosystem resilience has been largely neglected. A literature review was carried out across sectors (crop, livestock, aquaculture), both on the counterfactual, i.e., the lack of intraspecific diversity in the production system and on the direct and indirect roles that intraspecific diversity plays in maintaining seven of the regulating and supporting ecosystem services: (i) regulating pest and diseases; (ii) maintaining and regulating water and soil quality; (iii) regulating and improving the flow of reproductive diversity; (iv) buffering excess or lack of water; (v) regulating soil erosion; (vi) nutrient cycling in water and soil; and (vii) supporting habitat maintenance. Benefits from the use of intraspecific diversity, diversity per se, and adaptive traits include a limited use of chemical inputs and unsustainable practices and their negative impact on livelihoods, ecosystem functioning, and productivity. All sectors (crop, livestock, and aquaculture) should be examined in the agricultural production system to understand the provision of the different ecosystem services by intraspecific diversity. Differences in structure, functioning, and temporal and spatial scales of these sectors should also be considered. Supporting and regulating ecosystem services often have relatively longer-term processes than food provisioning and rely not only on the current diversity but also on its presence over time. The presented regulating and supporting ecosystem services rely on the presence of the diversity from the farm to the landscape and to agroecological zone. Neglecting the additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services is shown in this review to be detrimental to agricultural productivity and landscape resilience.