Otolith elemental signatures can be used to identify when individual or groups of fish are spending a significant amount of time in different environments. Elemental signatures of juvenile sardine Sardinops sagax caught in winter 2008 and 2009 around the coast of South Africa were measured using inductively-coupled plasma mass-spectroscopy. The otolith elemental signatures of 34 fish caught in 2008 and of 52 fish caught in 2009 were measured at the edge (to represent conditions 20-30 days prior to capture). Principal component analysis was used to visualise the relationships of individuals to each other, in terms of their otolith chemistry, in two-dimensional space, and multiple ANOVAs were used to investigate spatial and temporal variations among samples collected in 2008 and 2009. Significant differences among sites were found in MANOVAs, but the between-site differences varied among the elements. Magnesium concentration tended to decrease whereas barium concentration tended to increase from the west to the east coast. Barium indicate upwelling impact but for 2008 samples on the northern part of the west coast. Otolith microchemistry provides evidence of large and small-scale differentiation in sardine, but differences between years indicates that this is not necessarily temporally stable. The ocean off South Africa is a dynamic and variable environment and this is reflected in the inter-site, and also inter-annual, differences in elemental signatures of juvenile sardine.