The nymph Creusa bore him one son, Hypseus, who was King of the Lapiths, and three daughters, Menippe (mother of Phrastor by Pelasgus),Daphne and Stilbe. Some sources state that he was the father of Cyrene, alternately known as his granddaughter through Hypseus. Daphne, in an Arcadian version of the myth, was, instead, the daughter of the river god Ladon.
Peneus also had a son Atrax with Bura, and Andreus with an unknown consort.Tricce (or Tricca), eponym of the city Tricca, was mentioned as his daughter. In later accounts, Peneus was credited to be the father of Chrysogenia who consorted with Zeus and became the mother of Thissaeus. Meanwhile, his daughter Astabe coupled with Hermes and became the parents of Astacus, father of Iocles, father of Hipponous.
Eros shot Apollo with one of his arrows, causing him to fall in love with Daphne. It was Eros's plan that Daphne would scorn Apollo because Eros was angry that Apollo had made fun of his archery skills. Eros also claimed to be irritated by Apollo's singing. Daphne prayed to the river god Peneus to help her. He changed her into a laurel tree, which later became sacred to Apollo (see Apollo and Daphne). According to Hellanicus, Peneus was the father of Iphis, mother of Salmoneus by Aeolus the son of Hellen.