Developing a tool that identifies emotions based on their effect on cardiac activity may have a potential impact on clinical practice, since it may help in the diagnosing of psycho-neural illnesses. In this study, a method based on the analysis of heart rate variability (HRV) guided by respiration is proposed. The method was based on redefining the high frequency (HF) band, not only to be centered at the respiratory frequency, but also to have a bandwidth dependent on the respiratory spectrum. The method was first tested using simulated HRV signals, yielding the minimum estimation errors as compared to classic and respiratory frequency centered at HF band based definitions, independently of the values of the sympathovagal ratio. Then, the proposed method was applied to discriminate emotions in a database of video-induced elicitation. Five emotional states, relax, joy, fear, sadness, and anger, were considered. The maximum correlation between HRV and respiration spectra discriminated joy versus relax, joy versus each negative valence emotion, and fear versus sadness with p-value ≤ 0.05 and AUC ≥ 0.70. Based on these results, human emotion characterization may be improved by adding respiratory information to HRV analysis.