This thesis investigates the role of epistemic values, understood as methodological criteria of judgment, in two areas of evolutionary biology; behavioural ecology and paleontology. The focal point of the investigation on behavioural ecology is the debates on a cluster of problems related to the origin and maintenance of biological labour division, altruism, the theory of group selection vs. other kinds of selectionist accounts, and the handicap hypothesis concerning the reliability of biological signaling. The focal point of the investigation on paleontology is a cluster of problems that are all connected with the discussion on the evolutionary interpretation and significance of the Cambrian fossils of Burgess Shale, and include the scientific debates on their systematic interpretation, their morphological disparity, and the role of contingency in evolution. Based on a comparative study of publications connected to various scientific controversies in the two domains of inquiry it put forwards three general claims concerning the role of epistemic values in science that are empirically supported by the case studies: 1) There is a relation of reciprocal underdetermination between epistemic values and other important variables in the scientific process; 2) It is considerably easier for an individual scientist to convince other scientists of the validity of his of her conclusions if they are based on a set of values that are compatible with the dominant epistemic ideals of the scientific community of which the scientist is a member, and 3) the actions of individual scientists in scientific controversies constitute an important level of analysis in the investigation of epistemic values, where interesting phenomena occurs that may otherwise go unnoticed when focusing exclusively on the scientific collective. The existence of a relation of reciprocal underdetermination between epistemic values and other important epistemic variables is a serious hindrance for any universalist approach that attempts to establish the unification of the sciences on a uniform application of epistemic values. The dissent created by disagreements about how epistemic values are to be applied, is necessary in order to ensure a critical scrutiny of decisions that are based on these values.