This episode marks Alison Fox's only appearance as D'Argo's wife Lo'Laan. Rachel Gordon portrays Lo'Laan in Season 4's "Mental as Anything".
This is Grant Magee's first appearance as a young version of D'Argo's son Jothee, who he returned to play in "Rhapsody in Blue".
Crichton makes an oblique reference to a Hitchcock film being re-enacted. It is a reference to The Birds, based on Daphne Du Maurier's novel about flocks of birds that turn savage and attack.
D'Argo's backstory was changed in this episode. Prior to the series' start, a Rittenhouse Preview trading card indicated that a General D'Raam was jealous of D'Argo and was responsible for his downfall.
The revelation that Moya was pregnant was initially scripted to appear at the end of the "Premiere" episode.
This was Director Ian Watson's first episode behind the camera, brought in by first season producer Matt Carroll because of his skills working with actors to develop their characters.
The title "They've Got a Secret" is based on the long-running American game show I've Got a Secret which ran from 1952 into the 1970's.
Anthony Simcoe recalls that this episode was his favorite from the first season because of the depth that it gave D'Argo.
John: I am never going to get used to walking around inside a living ship.
Aeryn: You have nothing similar in your culture?
John: Well, Jonah and the whale, but no contemporary parallels. Except maybe the horse and rider.
Aeryn: Rider? The horse is a beast of burden?
John: Yeah. Not as large or sophisticated as Moya here, but kinda similar. Loyal and intelligent.
Aeryn: That you capture and make work for you.
John: Yeah, but we love them, too.
Aeryn: You love what you enslave?
John: We don't enslave them, all right? We... Fine, we enslave them.
D'Argo: Does it surprise you that such a Sebacean woman would love me?
Aeryn: D'Argo, it is ingrained in Peacekeepers from birth that we must keep the bloodlines pure. Such unions are evil.
D'Argo: Do you therefore think my son is evil?
Aeryn: No. Because in his eyes, I see you.