Improving the performance of underwater undulatory swimming (UUS) improves swimming time, so it is important to identify the pattern of muscle coordination in swimmers with fast UUS. This study aimed to identify muscular coordination in the trunk and lower limb during UUS in elite swimmers. Nine swimmers (aged 20 ± 2 years; height, 1.74 ± 0.03 m; weight, 73.0 ± 4.4 kg) participated in this study. Measurements were taken by electromyography of eight muscles: rectus abdominis (RA), internal abdominal muscle (IO), rectus femoris (RF), erector spinae (ES), multifidus (MF), tibialis anterior (TA), and thigh biceps (BF), and gastrocnemius (GS). For evaluation of muscle coordination, “muscle synergy” and “activation coefficient” were calculated using non-negative matrix factorization from electromyographic data. Kick frequency, kick amplitude, swim velocity, and kinematics of the pelvis were also calculated. Kick cycle was divided into two kick phases: downward kick (from the highest toe vertical coordinate to the lowest point) and upward kick (from the lowest point to the highest point). Kick frequency, kick amplitude, and swimming velocity were 1.9 ± 0.3 Hz, 0.45 ± 0.6 m, and 1.8 ± 0.2 m·s
−1
, respectively. The maximum backward pelvic tilt was 94.4 ± 4.5° and the minimum (forward) was 90.8 ± 5.7°. Three muscle synergy values were extracted from each swimmer during UUS: those involved in the transition from upward kick to downward kick (Synergy 1), downward kick (Synergy 2), and upward kick (Synergy 3). Synergy 1 involved mainly the RF, IO, and RA, which were activated during the turn from the upward to the downward phase. Synergy 2 involved mainly the MF, ES, and TA in the downward kick. Synergy 3 corresponded to the coordination of the BF and GS, which were active in the upward kick. In UUS by elite swimmers, both the upward kick and downward kick followed the trunk muscles involved in the pelvic forward–backward tilt movement, and lower limb muscles were activated. Muscle coordination based on pelvic forward-backward tilt during UUS is expected to contribute to the coaching field for elite swimmer development.