Methods to predict onset of cardio-pulmonary (CP) decompression sickness (DCS) would be of great benefit to clinicians caring for stricken divers. Principal dynamic mode (PDM) analysis of the electrocardiogram has been shown to provide accurate separation of the sympathetic and parasympathetic tone dynamics. Nine swine (Sus scrofa) underwent a 15 hour saturation dive at 184 kPa (60 ft. of saltwater) in a hyperbaric chamber followed by dropout decompression, while six swine, used as a control, underwent a 15 hour saturation dive at 15 kPa (5 ft. of saltwater). Non-invasive electrocardiograms were recorded throughout the experiment and autonomic nervous system dynamics evaluated by heart rate series analysis using power spectral density (PSD) and PDM methods. We observed a significant increase in the sympathetic and parasympathetic tones using the PDM method on average 20 minutes prior to DCS onset following a sudden induction of decompression. Parasympathetic activities remained elevated but the sympathetic modulation was significantly reduced at onset of cutis and CP DCS signs, as reported by a trained observer. Similar non-significant observations occurred during PSD analysis. PDM observations contrast with previous work showing neurological DCS resulted in >50% reduction in both sympathetic and parasympathetic tone. Therefore, tracking dynamics of the parasympathetic tones via the PDM method may allow discrimination between CP DCS and neurological DCS and this significant increase in parasympathetic tone has potential use as a marker for early diagnosis of CP DCS.