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High-intensity endurance exercise is linked to increased atrial fibrillation (AF) risk. P wave indices are established AF risk markers, but their role in ultramarathon athletes is unexplored. This study aimed to compare P wave indices between ultramarathon athletes and healthy controls. This cross-sectional study enrolled 74 ultramarathon athletes and 38 age- and sex-matched healthy volunteers (2:1 ratio). Athletes had completed ≥1 race of ≥100 km or ≥60 km in the past year. Participants with AF, atrial flutter, cardiovascular diseases, or structural heart abnormalities were excluded. Resting 12-lead ECGs evaluated P wave indices: maximum P wave duration, P wave dispersion, P wave terminal force in lead V1 (PTFV1), and P wave amplitude in lead II (PWAII). The cohort's mean age was 44.8 ± 8.2 years, 70% male. Ultramarathon athletes had significantly higher maximum P wave duration (114.24 ± 7.95 ms vs. 105.76 ± 7.15 ms, p < 0.001), P wave dispersion (18.77 ± 5.75 ms vs. 7.87 ± 2.51 ms, p < 0.001), PTFV1 (5795.66 ± 3212.27 μV·ms vs. 2399.17 ± 1140.19 μV·ms, p < 0.001) and PWAII (0.16 ± 0.05 mV vs. 0.12 ± 0.04 mV). Abnormal P wave duration (>120 ms) and PTFV1 (≥4000 μV·ms) were significantly more prevalent in ultramarathon athletes (25.7% vs. 5.3%, p = 0.010; 63.5% vs. 5.3%, p < 0.001). Similar findings were observed across genders. Ultramarathon runners demonstrate significant atrial electrical remodeling, as evidenced by abnormal P wave indices, may have potential relevance to arrhythmia risk. Further longitudinal studies are warranted to assess clinical outcomes.