Simple SummarySome species of sacoglossan sea slugs are able to steal chloroplasts from the algae they feed on and maintain them functional for several months, a process termed “kleptoplasty”. One of these photosynthetic slugs is Elysia crispata, found in coral reefs of the Gulf of Mexico. This sacoglossan inhabits different depths (0–25 m), being exposed to different food sources and contrasting light conditions. In this work, we characterized the pigment and fatty acid (FA) profiles, and quantified the total lipid, glycolipid and phospholipid contents of E. crispata from shallow (0–4 m) and deeper (8–12 m) waters, after a month of starvation to determine the longest and more stable retention of chloroplasts and its relation to habitat depth. Biochemical analyses allowed the identification of 12 photosynthetic pigments and 27 FAs. Heterogeneity in the composition of pigments confirmed the long-term retention of functional chloroplasts ingested from different algae. However, the differences found in pigment profile, total lipid content, and FA composition on individuals of E. crispata were not related to habitat depth. High amounts of glycolipids, exclusive chloroplast lipids, suggest a good condition of these photosynthetic organelles in animal cells. These results contribute baseline physiological data that may help explain evolutionary associations such as endosymbiosis.Long-term retention of functional chloroplasts in animal cells occurs only in sacoglossan sea slugs. Analysis of molecules related to the maintenance of these organelles can provide valuable information on this trait (kleptoplasty). The goal of our research was to characterize the pigment and fatty acid (FA) composition of the sea slug Elysia crispata and their associated chloroplasts that are kept functional for a long time, and to quantify total lipid, glycolipid and phospholipid contents, identifying differences between habitats: shallow (0–4 m) and deeper (8–12 m) waters. Specimens were sampled and analyzed after a month of food deprivation, through HPLC, GC-MS and colorimetric methods, to ensure an assessment of long-term kleptoplasty in relation to depth. Pigment signatures indicate that individuals retain chloroplasts from different macroalgal sources. FA classes, phospholipid and glycolipid contents displayed dissimilarities between depths. However, heterogeneities in pigment and FA profiles, as well as total lipid, glycolipid and phospholipid amounts in E. crispata were not related to habitat depth. The high content of chloroplast origin molecules, such as Chl a and glycolipids after a month of starvation, confirms that E. crispata retains chloroplasts in good biochemical condition. This characterization fills a knowledge gap of an animal model commonly employed to study kleptoplasty.