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Identifying exercise intensity boundaries has been shown to be important during endurance training for performance enhancement and rehabilitation. Unfortunately, even though surrogate markers show promise when assessed on a group level, substantial deviation from gold standards can be present in each individual. The aim of this study was to evaluate whether combining two surrogate intensity markers improved this agreement. Electrocardiogram (ECG) and gas exchange data were obtained from 21 participants who performed an incremental cycling ramp to exhaustion and evaluated for first (VT1) and second (VT2) ventilatory thresholds, heart rate (HR) variability (HRV), and ECG derived respiratory frequency (EDR). HRV thresholds (HRVT) were based on the non-linear index a1 of a Detrended Fluctuation Analysis (DFA a1) and EDR thresholds (EDRT) upon the second derivative of the sixth-order polynomial of EDR over time. The average of HRVT and EDRT HR was set as the combined threshold (Combo). Mean VT1 was reached at a HR of 141 ± 15, HRVT1 at 152 ± 14 (p < 0.001), EDRT1 at 133 ± 12 (p < 0.001), and Combo1 at 140 ± 13 (p = 0.36) bpm with Pearson's r of 0.83, 0.78, and 0.84, respectively, for comparisons to VT1. A Bland–Altman analysis showed mean biases of 8.3 ± 7.9, −8.3 ± 9.5, and −1.7 ± 8.3 bpm, respectively. A mean VT2 was reached at a HR of 165 ± 13, HRVT2 at 167 ± 10 (p = 0.89), EDRT2 at 164 ± 14 (p = 0.36), and Combo2 at 164 ± 13 (p = 0.59) bpm with Pearson's r of 0.58, 0.95, and 0.94, respectively, for comparisons to VT2. A Bland–Altman analysis showed mean biases of −0.3 ± 8.9, −1.0 ± 4.6, and −0.6 ± 4.6 bpm, respectively. Both the DFA a1 and EDR intensity thresholds based on HR taken individually had moderate agreement to targets derived through gas exchange measurements. By combining both non-invasive approaches, there was improved correlation, reduced bias, and limits of agreement to the respective corresponding HRs at VT1 and VT2. [ABSTRACT FROM AUTHOR]