Although the studied polymorphisms affect muscular proteins, aerobic adaptations, and recovery, their influence on the anthropometric variables and performance in ultramarathon runners is still poorly understood. This study aimed to determine the influence of ACTN3 R577X, ACE I/D, and CK MM A/G NcoI polymorphisms on the changes in the anthropometric variables and running time of 105 km mountain runners, in which 22 male Brazilian elite athletes (35.9 ± 6.5 years) were evaluated. Genotyping of the R577X (RR, RX, and XX), ACE I/D (DD, ID, and II), and CK MM A/G Ncol (AA, AG, and GG) polymorphisms was performed using the Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR-RFLP) technique with DNA extracted from saliva. Body composition was determined via bioimpedance. Pre- and post-race weight differences were observed on athletes with the AA genotype (77.1 ± 5.9 kg; 74.6 ± 5.6 kg) compared with those with the AG genotype (74.5 ± 8.0 kg; 68 ± 5.1 kg) (p = 0.02; p = 0.02). The RR genotype showed a correlation between BMI and running time (R = 0.97; p = 0.004). The genotype II showed a correlation with % fat and fat mass concerning running time (R = 0.91; p = 0.003; R = 0.99; p < 0.0001). The AA genotype was associated with post-race weight and lean mass loss, while the RR genotype correlated with BMI, and the genotype II correlated with % body fat and fat mass in relation to times in the 105 km mountain ultramarathon.