The aim of the present study was to examine the physiological and training characteristics in marathon runners with different sport experiences (defined as the number of finishes in marathon races). The anthropometry and physiological characteristics of men recreational endurance runners with three or less finishes in marathon races (novice group, NOV; n = 69, age 43.5 ± 8.0 years) and four or more finishes (experienced group, EXP; n = 66, 45.2 ± 9.4 years) were compared. EXP had faster personal best marathon time (3:44 ± 0:36 vs. 4:20 ± 0:44 h:min, p < 0.001, respectively); lower flexibility (15.9 ± 9.3 vs. 19.3 ± 15.9 cm, p = 0.022), abdominal (20.6 ± 7.9 vs. 23.8 ± 9.0 mm, p = 0.030) and iliac crest skinfold thickness (16.7 ± 6.7 vs. 19.9 ± 7.9 mm, p = 0.013), and body fat assessed by bioimpedance analysis (13.0 ± 4.4 vs. 14.6 ± 4.7%, p = 0.047); more weekly training days (4.6 ± 1.4 vs. 4.1 ± 1.0 days, p = 0.038); and longer weekly running distance (58.8 ± 24.0 vs. 47.2 ± 16.1 km, p = 0.001) than NOV. The findings indicated that long-term marathon training might induce adaptations in endurance performance, body composition, and flexibility.