This work aimed to develop a methodology for marking Artemia with different markers and evaluating their passage rate and digestibility in Lophiosilurus alexandri larvae of different ages. In the first phase, Artemia nauplii were marked 28 h after hatching with chromium oxide, titanium dioxide and NANOLIPE®. Contact times with the markers were 30, 60, 90 min at a concentration of 500 mg/L. Titanium dioxide had a higher concentration in Artemia than the other markers. The passage rate did not differ significantly between titanium and NANOLIPE®. In the second phase, the apparent digestibility of the protein in Artemia nauplii was evaluated for L. alexandri larvae at three ages. Average real protein digestibility at the three ages was 95.08%, demonstrating Artemia as a good quality food. All ages exhibited the same final time of fecal excretion of 30 min after feeding. Artemia nauplii presented satisfactory results for assimilation for all markers tested. In determining the digestibility of Artemia protein, we can conclude that chromium oxide and NANOLIPE® were good markers of animal metabolism and titanium dioxide was the worst marker of Artemia digestibility for the initial stages of L. alexandri.