Prolonged and repetitive breath-hold periods (apnea) during and sleep are a routine component in the ecological physiology of marine mammals. Seals are among the few mammals in which control of heart rate (HR) can be studied independent of respiration, without pharmacochemical manipulation. We hypothesized that the vasoactive hormones angiotensin II (Ang II), arginine vasopressin (AVP), and atrial natriuretic peptide (ANP) were involved in the control of cardiovascular function in seals, and that the relationship was dependent upon input from the respiratory system. Venous plasma samples were collected and electrocardiograms were recorded from Northern elephant seal (Mirounga angustirostris) and Weddell seal (Leptonychotes weddellii) pups during both spontaneous breathing (eupnea) and apnea. Instantaneous HR and simultaneous plasma levels of ANP, AVP, and Ang II from periods of eupnea and apnea were compared. In these seal pups, apnea was associated with bradycardia, increased ANP, and decreased AVP and Ang II. The results support the hypothesis of a complex involvement between the vasoactive hormones and the control of cardiovascular function, and provide evidence for differential levels of control during periods of eupnea and apnea.