Abstract Fish appear to have a limited capacity for digesting complex proteins during the early life stages. A better understanding of fish larvae protein digestive capacity and subsequent metabolic utilisation (amino acid (AA) catabolism and retention), depending on dietary protein molecular weight (MW) and larval development stages, is essential for developing formulated microdiets suited to larval requirements throughout ontogeny. The aim of this work was to develop a method enabling the in vivo production of radiolabelled polypeptides and protein fractions of different MW using Artemia metanauplii , and apply this new tool to assess protein digestive capacity and evaluate protein metabolic utilisation (catabolism and retention) throughout ontogeny of Senegalese sole larvae. Characterisation of MW distribution of Artemia protein content by size exclusion chromatography at different time points after hatching showed that from hatching to 24 h post-hatching (hph), the profile is dominated by polypeptides and proteins having a MW in the ranges 0.5–1.9 kDa, 2.8–7.0 kDa and above 476 kDa. At 36 hph a shift from high MW proteins to lower MW polypeptides was observed in the elution patterns. Fractions of radiolabelled polypeptides and proteins of various MW were produced through in vivo labelling of A. metanauplii , by incubation in a [U– 14 C] free AA mixture, and subsequent separation of Artemia proteins according to their MW by size exclusion chromatography. Digestibility and metabolic utilisation of some of the radiolabelled polypeptide fractions obtained (fractions of 1.0 kDa and 6.8 kDa) were assessed throughout Senegalese sole larval development (12, 21 and 34 days after hatching (DAH)) fed on live feed, through the controlled tube-feeding methodology combined with metabolic chambers. The results showed that the polypeptide fraction of 1.0 kDa was highly digestible and similarly retained in larval body at all developmental stages assayed. Conversely, the 6.8 kDa polypeptide fraction was poorly absorbed by young larval stages (12 DAH) but absorption improved throughout larval development (from 12 to 34 DAH). Body retention efficiency of the 6.8 kDa polypeptide fraction tended also to increase (and catabolism rate tended to decrease) throughout ontogeny, displaying a positive correlation (Spearman's correlation) with larval age. The method we report here is novel and may constitute a useful tool to assist in defining the most suitable MW range of proteins to incorporate into larval diets, for different developmental stages of Senegalese sole and other teleost larvae.