Motor sequences represent an integral part of human motor ability. Apart from simple movement sequences, complex coordinated movement sequences are the building blocks for peak athletic performance. Accordingly, optimized temporal and spatial coordination of muscle action across multiple limbs may be a distinguishing feature between athletes and non-athletes in many sports. In the present study, we aimed to assess differences between strength and endurance athletes and non-athletes during learning of a complex whole-body serial reaction time task (CWB-SRTT). For this purpose, 26 nonathletes (NAG) and 25 athletes (AG) learned the CWB-SRTT over 2 days separated by 7 days. Mean response times of participants were recorded and statistically analyzed for sequence-specific and non-sequence-specific improvements, as well as differences in learning rates and retention. Furthermore, AG was subdivided into strength (SG) and endurance (EG) athletes, and all analysis steps were repeated. Our results show a better mean response time of AG compared to NAG. However, we could not detect differences in sequence-specific or non-sequence-specific learning, as well as different retention rates between NAG and AG or SG and EG. We assume here that a potential lack of motor transfer between general athletic abilities and the specific complex motor sequence mainly accounts for our findings.