Harmful algal blooms (HABs) are highly relevant for public health, the economy, the ecosystem, and biodiversity stability in southern Chile (40° to 53°S), where they occur regularly and are frequently monitored. However, HAB events and their associated microbes in northern Chile (17° to 30°S) remain unknown and difficult to track due to a lack of monitoring, particularly in urban areas. We investigated changes in microbial communities in coastal seawater before and during an Akashiwo sanguinea bloom (B) at two sampling points in Antofagasta city (23°38'39S, 70°24'39W). Seawater samples (filtered at 1 and 0.2 μm) were collected during distinct bloom phases (control, prebloom, and in-bloom), and 16S and 18S rDNA gene libraries were constructed and analyzed via the DNA metabarcoding technique. Our findings indicate that species diversity within the 16S rDNA-based community was greater during the prebloom phase than during the control and in-bloom phases. Conversely, species diversity within the 18S rDNA-based community was lower during the in-bloom phase than during the control and prebloom phases. Independent of the sampling points and fractions, principal coordinate analysis (PCoA) revealed distinct differences in both the 16S and 18S rDNA-based communities between the analyzed bloom phases. Our analysis further revealed that the 16S rDNA-based community was dominated by the Flavobacteriaceae and Rhodobacteraceae families, whose abundance decreased and increased, respectively, during the bloom. As anticipated, the structure of the 18S rDNA-based community was predominantly governed by the Gymnodiniaceae family, specifically the Akashiwo genus, during the bloom. The differentiation in microbial communities was more pronounced in taxa with low abundances than in the dominant taxa. Additionally, co-occurrence network analysis revealed predominantly positive relationships within the microbial communities, particularly during the bloom event. Our analysis also identified several bacterial genera as keystone taxa within the microbial communities, notably members of Pseudomonadota and Bacteroidota.