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The Marduk Institute featured in Neon Genesis Evangelion is yet another instance of the creators seeding their work with references to mythology. This organization is mentioned as early as Evangelion Episode 01 and is "responsible" for selecting the Evangelion pilots. During Evangelion Episode 15 Ryoji Kaji is talking to his contact in the Japanese Government, he says "I know most of the names. Marduk Institute, a consultative firm established directly under The Human Instrumentality Committee in order to select the pilots of Evangelion." The names shown on the charter during that episode are as follows:

It is discovered that the Marduk Institute is just a front, there is no real Institute, Gendou and company are pulling all the strings. During Evangelion Episode 17, Toji Suzuhara is chosen as the Fourth Children. Misato asks why he was chosen, and Ritsuko says "We had no choice. The candidates have been gathered in one place, and are being protected.", later in that episode Kaji tells Misato that the Marduk Institute doesn't exist and that she should investigate "Code 707", Shinji's school.

From this it is clear that the Marduk Institute is just a front, that NERV grouped all potential pilots together in Shinji's class, and then selects the ones it needs from that group.