In this paper, we develop a robust palaeo-proxy technique for inferring seasonal fluctuations in Phanerozoic seawater temperature. Specifically, we report ��13C and ��18O values across the columnar layer (inner shell) of Permian brachiopods, including five genera of the Order Spiriferida (Ingellarella, Martinia, Permophricodothyris, Cartorhium, and Trigonotreta) and two genera of the Order Athyridida (Araxathyris and Comelicania). These brachiopod specimens are inferred to have inhabited varied palaeo-depths, based on facies analysis, and were collected from low, middle and high palaeolatitudes. To obtain high-resolution ontogenetic isotopic time-series, a handheld microdrill was used to collect low-magnesium calcite samples along the longitudinal axis of the mid-valve for each specimen. Intrageneric and intergeneric comparison of statistics (mean values, variance, and range) reveals that ��18O values are consistent within and between genera although ��13C values are more variable. In specimens obtained from low palaeolatitudes (Julfa Formation, Iran; Bellerophon Formation, Italy; Late Permian), the range of ��18O values is small and consistent with weak seasonal temperature variations, irrespective of water depth. In specimens obtained from middle palaeolatitudes (Qarari Formation, Oman; Early-Middle Permian), we found a range of ��18O values dependent on inferred water depth, possibly reflecting a change in thermocline structure between warm and cold seasons. In specimens obtained from high palaeolatitudes (Wasp Head and Wandrawandian Siltstone formations, Australia; Early-Middle Permian), brachiopods from glacial and interglacial climate phases show significant variations of ��18O values, probably caused by seasonal changes in the seawater surface temperature. Based on these findings, the technique developed in this paper appears to provide reliable paleoclimate and paleoenvironmental data for Permian sites, and should be also applicable for Phanerozoic studies in general. However, we caution that ��18O values vary dependent on the growth direction, resulting in differences of up to 5 ��C in seawater paleotemperature calculations, and emphasise that a consistent sampling strategy accounting for shell structure and growth direction is required.