Changes in total lipids and fatty acid profiles (FAPs) of gonad, digestive gland, mantle and muscle of the tropical scallop Nodipecten nodosus were examined during coastal upwelling and upwelling relaxation periods. Total lipids were most abundant in digestive gland, and intermediate in female gonad. Multidimensional scaling analysis of similarities (MDS-ANOSIM) and similarity percentage analyses (SIMPER) revealed significant changes of FAPs of the four tissues during the upwelling and upwelling relaxation periods. During both periods, SIMPER analysis revealed an internal similarity index greater than 90% for FAP of each tissue. However, during upwelling the gonad-FAP showed a lower dissimilarity index with the digestive gland-FAP (10), than with muscle-FAP (11) or mantle-FAP (13). In general, during upwelling, the fatty acids 16:0, 18:0, 16:1 n-7, 20:5n-3, 22:6n-3 and total PUFAn-3 explained 42 to 63% of variance between tissues; during upwelling relaxation, these fatty acids together with 14:0 and 18:1 n-7, explained 46 to 64% of variance. During upwelling period, MDS-ANOSIM showed a close association between FAP of digestive gland and gonad, suggesting a rapid transfer of fatty acids between these tissues, and consequently, that N. nodosus follows an opportunistic strategy during this period. In contrast, during upwelling relaxation, the slow and continuous fall in total lipid contents of digestive gland (September to November) and the progressive reduction of MDS distances between FAPs of digestive gland and gonad (August until November), suggest a gradual transfer of lipids from digestive gland to gonad to support the gonad development observed during this period. This suggests that N. nodosus switches to a conservative strategy during the upwelling relaxation period.