Mango genotypes can be classified as monoembryonic or polyembryonic. In order to understand the role of metabolites in the ovaries formation in mango genotypes, the present study was conducted. In this regard, the metabolite diversity was assessed in ovaries of monoembryonic and polyembryonic mango genotypes at various stages and also attempted to identify the stages of segment formation in the ovary of polyembryonic genotypes. The study on segment formation was carries out in polyembryonic genotypes (Vellaikolumban and Olour) at different stages of ovary development i.e. starting from pre anthesis, one day after anthesis, 1st, 2nd and 3rd week after anthesis. Clear segments were observed in one month old fruits. No segments were visible before that. Therefore, the segment formation may occur in between 3rd week to 4th week after anthesis. Profiling of metabolites was done in 2 monoembryonic and 2 polyembryonic genotypes and at different stages of development of ovary i.e. before anthesis, one day after anthesis, 1st, 2nd and 3rd week after anthesis. All the polyamines, amino acids and sugars were more in monoembryonic genotypes indicating that these metabolites may not be responsible for the formation of multiple embryos. The phytohormones such as SA, IAA, IBA, GA7, GA4 and zeatin were found to be high in polyembryonic mango genotypes except ABA and ACC. ABA and ACC are high in monoembryonic mango genotypes. The metabolite analysis of ovaries in polyembryonic genotypes indicated that the formation of multiple embryos in mango may be more closely related to the higher concentration of IAA, IBA, and SA.