The present study examined site-specific hamstring muscles use with functional magnetic resonance imaging (MRI) in elite soccer players during strength training. Thirty-six players were randomized into four groups, each performing either Nordic hamstring, flywheel leg-curl, Russian belt or the hip-extension conic-pulley exercise. The transverse relaxation time (T2) shift from pre- to post-MRI were calculated for the biceps femoris long (BFl) and short (BFs) heads, semitendinosus (ST) and semimembranosus (SM) muscles at proximal, middle and distal areas of the muscle length. T2 values increased substantially after flywheel leg-curl in all regions of the BFl (from 9±8 to 16±8%), BFs (41±6-71±11%), and ST (60±1-69±7%). Nordic hamstring induced a substantial T2 increase in all regions of the BFs (13±8-16±5%) and ST (15±7-17±5%). T2 values after the Russian belt deadlift substantially increased in all regions of the BFl (6±4-7±5%), ST (8±3-11±2%), SM (6±4-10±4%), and proximal and distal regions of BFs (6±6-8±5%). T2 values substantially increased after hip-extension conic-pulley only in proximal and middle regions of BFl (11±5-7±5%) and ST (7±3-12±4%). The relevance of such MRI-based inter- and intra-muscle use in designing more effective resistance training for improving hamstring function and preventing hamstring injuries in elite soccer players should be explored with more mechanistic studies.