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Many giant dsDNA algal viruses share a common ancestor with Mimivirus -one of the largest viruses' in terms of genetic content. Together' these viruses form the proposed 'Megaviridae' clade of nucleocytoplasmic large DNA viruses. To gauge Megaviridae diversity' we designed degenerate primers targeting the major capsid protein genes of algae-infecting viruses within this group and probed the clade's diversity during the course of a brown tide bloom caused by the harmful pelagophyte' Aureococcus anophagefferens. We amplified target sequences in water samples from two distinct locations (Weesuck Creek and Quantuck Bay' NY) covering 12 weeks concurrent with the proliferation and demise of a bloom. In total' 475 amplicons clustered into 145 operational taxonomic units (OTUs) at 97% identity. One OTU contained 19 sequences with ⩾97% identity to AaV' a member of the Megaviridae clade that infects A. anophagefferens' suggesting AaV was present during the bloom. Unifrac analysis showed clear temporal patterns in algal Megaviridae dynamics' with a shift in the virus community structure that corresponded to the Aureococcus bloom decline in both locations. Our data provide insights regarding the environmental relevance of algal Megaviridae members and raise important questions regarding their phylodynamics across different environmental gradients. [ABSTRACT FROM AUTHOR]