This study establishes the blood reference intervals (RIs) for clinically healthy and farmed juvenile Asian seabass (Lates calcarifer), within 4–6 weeks after stocking into flow‐through, marine aquaculture systems. The 90% percentile RIs (n = 156, mean bodyweight 41.8 g) are as follows: glucose (GLU) 2.4–11.3 mmol/L, haematocrit (Hct) 18.9%–39.2%, haemoglobin concentration (Hb) 56.0–85.0 g/L, total plasma protein (TPP) 56.0–77.0 g/L, total red blood cell (RBC) count 4.1–11.2 × 1012/L, total white blood cell (WBC) count 5.3–69.9 × 109/L, total lymphocytes 4.7–51.4 × 109/L, monocytes 0.3–16.2 × 109/L and heterophils count 0.6–8.4 × 109/L. Pearson's method analysis showed weak but significantly positive correlations between fish bodyweight and Hct, Hb, TPP and total RBC count (p < 0.05). Histopathology of 42 of the 156 clinically healthy fish used to derive the RIs, with blood values within the 90% percentile range, did not exhibit any abnormal pathology. In contrast, histopathology from a different group of clinically healthy L. calcarifer (n = 72, mean bodyweight 31.3 g) with blood values falling outside of these established 90% percentile RIs showed that 25% of these fish had severe, chronic granulomatous enteritis, and 13% had severely depleted lipid stores in their liver. Point biserial correlation analysis of blood values from this second group of 72 fish showed that elevated total WBC, monocyte and heterophil counts and reduced Hct levels are significantly associated (p < 0.05) with the occurrence of severe, chronic granulomatous enteritis and depleted lipid stores in their liver. Reduced blood GLU and TPP levels in the second group of fish were significantly associated with fish that had depleted lipid stores in liver (p < 0.05), corroborating a period of malnutrition. This study is among the first to establish blood RIs for clinically healthy, farmed juvenile L. calcarifer and detection of subclinical diseases in fish to support early intervention.