Acute life-threatening situations are particularly critical when superimposed on chronic diseases. The objective of this study was the assessment of heart rate (HR) dynamics during episodes of acute anoxia superimposed on a rat model of chronic pulmonary hypertension. In 10 adult Wistar rats, five weeks after pulmonary hypertension induction with Monocrotaline, we analysed eight 1-min HR segments, during episodes of baseline, mechanical ventilation and acute anoxia, using linear indices, approximate entropy (ApEn), sample entropy (SampEn) and multiscale entropy (MSE). The transition from baseline or mechanical ventilation to early anoxia was identified through almost all indices, but SampEn(2,0.6) was the index that better identified all the transitions. MSE presented limited performance, possibly due to the non-stationary nature and short duration of the acute anoxia episodes. A systematic evaluation of all computed HR indices may help to identify which indices or combination of indices more adequately discriminates and monitors critical acute events superimposed on chronic clinical conditions.