Searching for molluscicidal agents of biological origin is mandatory to avoid the drawbacks of using chemical molluscicides. Algae are good candidates as sources of compounds with molluscicidal properties, especially if they are combined with modern techniques such as nanotechnology. This study aimed to evaluate the molluscicidal activity of two algal extracts and their biosynthesized zinc oxide nanoparticles (ZnONPs) on Biomphalaria alexandrina snails. The results indicated that the lowest LC50 was that of Spirulina platensis extract followed by Scenedesmus obliquus extract. Subchronic experiments were conducted for 2 weeks to indicate the effect of LCo of S. obliquus and S. platensis extracts, and 1/4 LCo of ZnONPs synthesized by S. obliquus and that synthesized by S. platensis. Histopathological alterations were observed in the digestive and hermaphrodite glands of treated snails. Also, random amplified polymorphic DNA-polymerase chain reaction indicated genotoxic effects in the DNA of treated snails, as 1/4 LCo of ZnONPs synthesized by S. obliquus was the most effective treatment. The toxicity assay using Artemia salina indicated that the effective concentrations on B. alexandrina snails were safe on other non-target organisms. © 2022 John Wiley & Sons Ltd.