The Mokonas were created by Yūko Ichihara and Clow Reed, who appear to be aware of the existence of Sakura Kinomoto and all of the events in her world. One day, Yūko and Clow encountered the original Mokona, who was traveling through different worlds. Mokona provided Yūko and Clow with the knowledge of alternate dimensions. After learning that one day a Sakura and Syaoran from an alternate world would come to their world to ask for help, Yūko and Clow created the two Mokona, basing them on the original-Mokona of Cephiro from Magic Knight Rayearth- but with slight differences, such as difference in size and the ability to talk (whereas the original Mokona would only say "Puu!"). Each Mokona was also given an earring which matched the color of the gem on its forehead, the blue earring seals magic power while the red earring boosts magic power. It has never been discovered what exactly a Mokona is. The original Mokona was identified as the creator of the universe, but it is unknown whether the original was part of a species or not, which also raises the question as to where the name Mokona came from in the first place?
In the book, Soel to Larg: Mokona=Modoki no bouken, there is a explanation given for the "Modoki". This prefix means "pseudo", meaning "false mokona", "copy of mokona". Because the Mokonas were a creation from the realMokona from Magic Knight Rayearth.