There is an intriguing system for sex determination in Carica Papaya. To explain the genetics of the Papaya’s sex determination there were many hypotheses based on information and knowledge from time to time. Such information and knowledge were about a generic balance of sex autosomes and chromosomes, Classical XY Chromosomes. Nowadays determination of molecular level through genomic technology is possible. Predicted hypotheses can be proving by high density linkage mapping. It shows that with small specific region (MSY) of Y chromosome sex determination can be controlled by a pair of primitive sex chromosomes. It proves that two sex determination genes can control the whole pathway of sex determination. Feminizing or stamen suppressor gene, cause absorption before a flower inception with other while masculinising or carpel suppressor genes cause carpel absorption at the development stage of the flower. To reveal the structural details of sex determination region and sequencing of candidate sex determination genes physical mapping is essential. This process can be observed while papaya production. Progress in Chemical and Biochemical Research (PCBR)