Harmful algal blooms (HABs) represent a considerable ecological threat to coastal waters globally. Certain toxigenic microalgae produce phycotoxins that can accumulate and transfer through the food web, thereby posing risks to marine ecosystems and human health. This study summarized the spatial and temporal distribution patterns of marine algal toxins in shellfish from the Guangxi coastal area of the Beibu Gulf, a key aquaculture region in China. Elevated toxin levels were particularly noted for marine algal toxins such as domoic acid (DA), gymnodimine-A (GYM-A), and spirolide-1 (SPX1). Relatively high levels of DA occurred in shellfishes from March to August, while slightly higher contents of GYM-A and SPX1 in shellfish emerged in October and December. Fortunately, samples contained DA levels below the safety standards for seafood consumption, but no regulatory limits have been established for GYM-A and SPX1. The research also identified various algal toxins in the phytoplankton of the whole gulf, with pollution levels in the northern region significantly higher than those in the Qiongzhou Strait and southern waters. Additionally, a small database of toxic algae was established, isolating and culturing 11 monoclonal strains identified as belonging to 7 species, including the toxin-producing Alexandrium pacificum. This study provides essential data and methodological support for monitoring algal toxins in the Beibu Gulf.