Abstract Individual specialization in the foraging behaviour of marine predators can affect the ecology, evolution, and ability of a population to respond to environmental variability and human impacts. Here, blood serum and whisker stable isotope values from New Zealand (NZ) sea lion pups (Phocarctos hookeri) are compared with their mother’s values to identify whether they can be used as proxies to identify their mother’s isotopic niche and foraging strategy. Female NZ sea lions have been identified, both through telemetry and stable isotope research of blood serum and whiskers, to have two distinct foraging ecotypes (mesopelagic or benthic), consistent across their adult life. Females who are mesopelagic foragers have higher overlap and a greater risk of harmful interactions with fisheries. Stable isotope analysis of adult females can be used to determine the proportion of the female population exposed to these detrimental interactions. However, the capture, restraint, and removal of a whisker or blood from an adult female NZ sea lion is an expensive, time‐consuming, and invasive undertaking. Instead, by comparing the blood serum and whisker δ13C and δ15N values of 12 NZ sea lion mother‐and‐pup pairs, for whom the foraging behaviour of the female is known, the question as to whether a pup’s blood serum or whisker isotope value can be used as a proxy to identify female foraging ecotype was investigated. The δ13C and δ15N values for the blood serum and whiskers of pups and their mothers were correlated and differed significantly between foraging ecotypes. This research validates that pup blood serum and whisker stable isotope values from 1‐month‐old pups can be used as indicators of female isotopic niche and therefore foraging ecotype. This tool can be used across all NZ sea lion colonies to indicate female NZ sea lion foraging ecotypes. For the Auckland Islands, it could determine the proportion of breeding females exposed to negative interactions with fisheries, leading to a better understanding of the level of these effects and helping to implement appropriate management to mitigate impacts.