This study aimed to clarify the differences in muscular coordination during butterfly swimming between high- and low-performance swimmers using muscle synergy analysis. Eight female competitive swimmers and 8 female recreational swimmers participated in this study. The participants swam a 25-m butterfly stroke with maximum effort. Surface electromyography was measured from 12 muscles and muscle synergy analysis was performed from the data using nonnegative matrix factorization algorithms. From the results of the muscle synergy analysis, 4 synergies were extracted from both groups. Synergies 1 and 2 were characterized by coactivation of the upper and lower limb muscles in the recreational swimmers, whereas only synergy 1 was characterized by this in the competitive swimmers. Synergy 3 was involved in arm recovery in both groups. Synergy 4 was only involved in the downward kick in the competitive swimmers. From these results, it can be concluded that muscle synergies with combined coordination of upper and lower limb muscles were extracted more in the recreational swimmers and that the competitive swimmers controlled the downward kick with an independent synergy and that the adjustment of the timing of the downward kick may be an important factor for the efficient performance of butterfly swimming.