Joaquin Rafael Bottom was born on October 28, 1974, at the Hospital Metropolitano San Francisco in the Río Piedras district of San Juan, Puerto Rico, to John Lee Bottom, the founder of a landscape gardening company, and Arlyn "Heart" Bottom (née Dunetz), who was an executive secretary at NBC and whose connection to an agent provided her children with acting work. He is the third of five children, following River (1970–1993) and Rain (born 1972), and preceding Liberty (born 1976) and Summer (born 1978), all of whom have been involved in acting. Phoenix also has a paternal half-sister, Jodean (born 1964). His father was a Catholic from Fontana, California, and was of English, German and French ancestry. His maternal grandfather, Meyer Dunetz, was Russian Jewish and his maternal grandmother, Margit Lefkowitz, was Hungarian Jewish; they were both Ashkenazi Jews who resided in New York City. Phoenix's parents met when his mother was hitchhiking in California, and they got married less than a year after meeting.
Soon after the second child was born, they joined the religious cult called Children of God and started traveling throughout South America and Puerto Rico in the Caribbean as missionaries for the cult, where the next two children were born. They eventually grew disillusioned with Children of God and left in 1977, being opposed to the cult's increasingly distorted rules, particularly the practice of flirty fishing. The fifth child was born in Florida where the family settled for a while. It was also around this time they legally adopted the surname Phoenix, inspired by the mythical bird that rises from its own ashes, symbolizing a new beginning. When Phoenix was three, he and his older siblings witnessed fish being stunned as "they were throwing them against the side of the boat." This act made the whole family convert to a vegan lifestyle. He also began calling himself "Leaf", having been inspired by spending time outdoors raking leaves and desiring to have a nature-related name like his siblings. Leaf became the name he used before changing it back to his birth name Joaquin at the age of fifteen.