Several recent investigations showed that the best marathon time of an individual athlete is also a strong predictor variable for the race time in a 100-km ultra-marathon. We investigated similarities and differences in anthropometry and training characteristics between 166 100-km ultra-marathoners and 126 marathoners in recreational male athletes. The association of anthropometric variables and training characteristics with race time was assessed by using bi- and multi-variate analysis. Regarding anthropometry, the marathoners had a significantly lower calf circumference (P < 0.05) and a significantly thicker skinfold at pectoral (P < 0.01), axilla (P < 0.05), and suprailiacal sites (P < 0.05) compared to the ultra-marathoners. Considering training characteristics, the marathoners completed significantly fewer hours (P < 0.001) and significantly fewer kilometres (P < 0.001) during the week, but they were running significantly faster during training (P < 0.001). The multi-variate analysis showed that age (P < 0.0001), body mass (P = 0.011), and percent body fat (P = 0.019) were positively and weekly running kilometres (P < 0.0001) were negatively related to 100-km race times in the ultra-marathoners. In the marathoners, percent body fat (P = 0.002) was positively and speed in running training (P < 0.0001) was negatively associated with marathon race times. In conclusion, these data suggest that performance in both marathoners and 100-km ultra-marathoners is inversely related to body fat. Moreover, marathoners rely more on speed in running during training whereas ultra-marathoners rely on volume in running training.