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Abstract Chiffon is the soleDrosophilaortholog of Dbf4, the regulatory subunit for the cell‐cycle kinase Cdc7 that initiates DNA replication. InDrosophila, thechiffongene encodes two polypeptides with independent activities. Chiffon‐A contains the conserved Dbf4 motifs and interacts with Cdc7 to form the Dbf4‐dependent Kinase (DDK) complex, which is essential for a specialized form of DNA replication. In contrast, Chiffon‐B binds the histone acetyltransferase Gcn5 to form the Chiffon histone acetyltransferase (CHAT) complex, which is necessary for histone H3 acetylation and viability. Previous studies have shown that the Chiffon‐B region is only present within insects. However, it was unclear how widely the interaction between Chiffon‐B and Gcn5 was conserved among insect species. To examine this, we performed yeast two‐hybrid assays using Chiffon‐B and Gcn5 from a variety of insect species and found that Chiffon‐B and Gcn5 interact in Diptera species such as Australian sheep blowfly and yellow fever mosquito. Protein domain analysis identified that Chiffon‐B has features of acidic transcriptional activators such as Gal4 or VP16. We propose that the CHAT complex plays a critical role in a biological process that is unique to Dipterans and could therefore be a potential target for pest control strategies.