The purpose of this study was to assess the influence of scapular alignment on the electromyographic (EMG) activity of the trapezius in people with a short pectoralis minor muscle. For the study, we recruited 15 volunteers who had positive results for short on a pectoralis minor muscle length test. We measured the EMG activity of the upper, middle and lower trapezius muscles. The participants lifted their dominant arm to ear level with the thumb up toward the ceiling in the prone position on a table with the shoulder at a flexion angle of 180 degrees and a horizontal abduction angle of 120 degrees. Scapula was manually aligned by an experienced physical therapist prior to arm lift for the scapular alignment condition. A paired t-test was used to compare the effects of scapular alignment on the EMG activity of the trapezius muscles. The EMG activity of the lower trapezius muscle was significantly increased during the test with the scapular alignment compared to that without scapular alignment (p<.05), while the upper trapezius and middle trapezius exhibited no significant difference between the two conditions (p>.05). The findings of this study suggest that a scapular alignment may alter the recruitment of the lower trapezius muscle during arm lifting in the prone position in people with a short pectoralis minor muscle.