Two Parthenium hysterophorus populations resistant (R) and susceptible (S) harvested in banana crop from the Dominican Republic were studied. All S plants died when the herbicides were applied at field dose, except with paraquat. For the R population, the order of plant survival was as follows: glyphosate and paraquat > flazasulfuron > glufosinate > fomesafen > 2,4-D. The resistance factors obtained in the dose–response assays showed a high resistance to glyphosate, flazasulfuron, and fomesafen, medium resistance to glufosinate and 2,4-D, and a natural tolerance to paraquat (resistance factor (RF) = 1.0). The I50 values obtained in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), acetolactate synthase (ALS), and glutamine synthetase (GS) activity studies with glyphosate, flazasulfuron, and glufosinate, respectively, were greater in R than in S. The effect of fomesafen was measured by the Proto IX levels, obtaining five times more Proto IX in the S than in the R population. The resistance to 2,4-D in the R was determined by the lower accumulation of ethylene compared to the S population. The studies with 14C-paraquat conclude that the lower absorption and translocation in both the R and S populations would explain the natural tolerance of P. hysterophorus. This is the first case of multiple resistance to herbicides with different mechanisms of action confirmed in P. hysterophorus.