Iain de Caestecker and Elizabeth Henstridge were representing their fellow Agents of S.H.I.E.L.D. at New York Comic Con this weekend and had the opportunity to dispel a fan rumor. Despite the characters' close, familiar relationship, Fitz and Simmons are not brother and sister.
When someone in the audience Q&A asked about the techies' easily misinterpreted relationship, the actors laughed. De Caestecker agreed that the two often act like siblings, but also pointed out that Henstridge thinks they have an "old married couple" quality. Neither married nor blood-related, the backstory is that the characters have simply known each other for long enough to have developed a professional and personal shorthand. You know what this means, internet. Feel free to ship and fan fic away, and check out the promo for episode four below.