Sturgeon broodstock management includes unavoidable handling and surgery procedures such as biopsy, endoscopy, laparotomy, oviduct incision inducing stress response. Clove oil and 2‐phenoxyethanol (2‐PE) are anesthetics commonly used in aquaculture to reduce the stress. The present study aimed to determine the anesthetic efficiency, hematological, histopathological and echocardiographic effects of clove oil and 2‐PE in adults Danube sturgeon (Acipenser gueldenstaedtii). Experimental fish were exposed to anesthetic baths to 20, 40 and 80 μl/L clove oil and 250, 500 and 750 μl/L 2‐PE concentrations and the induction‐recovery timed were recorded. The induction and recovery times in Danube sturgeon were significantly affected by clove oil and 2‐PE concentrations. The results showed that 2‐PE at 250–500 μl/L concentration failed to induce anesthesia; however, 750 μl/L concentrations induced anesthesia within 290 s. The optimum concentrations of clove oil showed in the present work were between 40 and 80 μl/L concentrations induced anesthesia within 180–120 s. The anesthetized fish showed alteration in hematological and echocardiographic indices was time dependent. RBC, HCT and LYM values in 40 and 80 μl/L clove oil and 750 μl/L 2‐PE groups were significantly lower than control group in 4th h. The mean heart rates were significantly affected before and after anesthesia treatment at clove oil. Whereas, no significant changes were observed in mean heart rates for 2‐PE. Fish anaesthetized with clove oil or 2‐PE exhibited histopathological deformity symptoms in the gill compared to control groups. In conclusion, the present study demonstrated that minimum effective concentration of clove oil was 40 μl/L for short‐term anesthesia, but 80 μl/L concentration is suitable for deep anesthesia. 2‐PE may not be suitable for adult Danube sturgeon due to long induction time and high concentration. It is also concluded that higher anesthetic concentrations may have detrimental effects on the fish gill tissue.