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The biochemical composition, molecular diversity, and two different bioactivities of <i>Asparagopsis armata</i> and <i>Rugulopteryx okamurae</i> (two alien species with different invasive patterns in the southern Iberian Peninsula) were analyzed through spectrophotometric methods and Fourier transform ion cyclotron mass spectroscopy (FT-ICR-MS). A total of 3042 molecular formulas were identified from the different extracts. The _dH₂O extracts were the most molecularly different. <i>A. armata</i> presented the highest content of nitrogenous compounds (proteins, CHON) and sulphur content, whereas <i>R. okamurae</i> was rich in carbonated compounds (total carbon, lipids, CHO, and CHOP). Antioxidant capacity and phenolic content were higher in <i>R. okamurae</i> than in <i>A. armata</i>. Antimicrobial activity was detected from both species. <i>A. armata</i> showed capacity to inhibit human and fish pathogens (e.g., <i>Staphylococcus aureus</i> or <i>Vibrio anguillarum</i>), whereas <i>R. okamurae</i> only showed inhibition against human bacteria (<i>Staphylococcus aureus</i> and <i>Cutibacterium acnes</i>). In <i>R. okamurae</i>, molecules with a great number of pharmaceutical activities (e.g., anti-inflammatory or antitumoral), antibacterial, biomaterial, and other utilities were found. The main molecules of <i>A. armata</i> had also pharmaceutical applications (e.g., antimalarian, antithrombotic, anti-inflammatory, or antiarthritis). The valorization of these species can help to counteract the environmental effects of the bioinvasions.