The stress assignment system of contemporary Mapudungun (a.k.a. Araucanian) has long been controversial. This paper reconsiders the system in the light of morphological structure, contrasting the present-day data with the sparse but suggestive historical record spanning 1606-1916. I argue that Mapudungun has undergone changes both to the metrical and morphological domains determining stress position. I show that early lack of weight-sensitivity is quickly replaced by a decidedly weight-sensitive system and that stress appears to have changed from marking the edge of verbal roots, to marking the edge of stems. Crucially, however, certain aspects of the system-such as right-alignment of prosodic units and the left-headedness of feet-show pertinacity: lack of change despite surface alternations. I conclude that stress assignment in Mapudungun is subordinate to morpho-phonological transparency both synchronically and diachronically, such that the hierarchy and position of stress may vary in order to highlight elements of the language’s polysynthetic, agglutinating morphology.