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The congeneric approach assesses the relative role of exotic invasive plants compared to native plants on associated species. However, most studies on seed germination have been conducted in Petri dishes that do not reflect natural soil conditions. Here, we compared the effects of different litter extracts of the exotics Prosopis juliflora (Sw.) DC. and Prosopis pallida (Willd.) Kunth, as well as native Prosopis cineraria (L.) Druce, on seed germination and seedling dry weight of two weedy plants (Amaranthus graecizans L. and Sisymbrium irio L.) and the native Senecio flavus (Decne.) Sch.Bip. in both Petri dishes and potted soil experiments. The results indicate that non-treated seeds (control) of the three species attained more than 95% germination in the Petri dishes (in vitro). The increase in the litter concentrations of both invasive Prosopis species inhibited the native Senecio flavus germination and significantly reduced germination and seedling weight of the weedy A. graecizans and Sisymbrium irio. Nevertheless, the native P. cineraria extracts had significant depressive effects on seed germination and seedling growth of the native Senecio flavus but limited effects on the weedy A. graecizans and Sisymbrium irio. The results support a greater impact of exotic than native congener on native plants. To better assess allelopathic effects, it is recommended to not rely on germination in Petri dishes.