The aim of this paper was to examine the phonology of suffixation and prefixation in Malay, particularly the phonological alternations that are derived due to the morphological process of affixation. It is apparent that the phonological behaviour of suffixation in this language is quite distinct, both in terms of character and degree of generality from prefixation. Rules that are visibly active at the stem-prefix juncture are not permissible at the stem-suffix juncture, and vice versa. This asymmetry has not been satisfactorily accounted for in previous works. The present analysis attempted to account for this irregularity by adopting the theoretical framework of Optimality Theory (Prince & Smolensky, 2004). The apparent irregularity is accounted for as a consequence of a candidate output satisfying more dominant constraints in the hierarchy. The relevant constraints that play significant roles here are the alignment constraints of the prosody-morphology interface, which require that the edge of some grammatical category coincide with the edge of some prosodic category. The prefix-stem boundary is controlled by ALIGN-PREF, requiring that the right edge of a prefix coincides with the right edge of a syllable, while the stem-suffix boundary is governed by ALIGN-SUF, requiring that the left edge of a suffix coincides with the left edge of a syllable, and ALIGN-STEM, requiring that the right edge of a stem coincide with the right edge of a syllable. ALIGN-SUF and ALIGN-STEM are higher ranked than ALIGN-PREF in the hierarchy. This schematic ranking straightforwardly explains the irregularity in the prefixation and suffixation in Malay.