Twintrons were discovered by Donald W. Copertino and Richard B. Hallick as a group II intron within another group II intron in Euglena chloroplast genome. They found that splicing of both the internal and external introns occurs via lariat intermediates. Additionally, twintron splicing was found to proceed by a sequential pathway, the internal intron being removed prior to the excision of the external intron.
Since the original discovery, there have been other reports of Group III twintrons and GroupII/III twintrons in the chloroplast of Euglena gracilis. In 1993 a new type of complex twintron composed of four individual group III introns has been characterized. The external intron was interrupted by an internal intron containing two additional introns. In 1995 scientists discovered the first non-Euglena twintron in cryptomonad alga Pyrenomonas salina. In 2004, several twintrons were discovered in Drosophila.