The postharvest properties of two ultra-late maturing peach cultivars, “Tobihaku” (TH) and “Daijumitsuto” (DJ), were investigated. Fruit were harvested at commercial maturity and held at 25°C. TH exhibited the characteristics of normal melting flesh (MF) peach, including rapid fruit softening associated with appropriate level of endogenous ethylene production In contrast, DJ did not soften at all during 3 weeks experimental period even though considerable ethylene production was observed. Fruit of TH and DJ were treated with 5,000 ppm of propylene, an ethylene analog, continuously for 7 days. TH softened rapidly whereas DJ maintained high flesh firmness in spite of an increase in endogenous ethylene production, suggesting that DJ but not TH lacked the ability to be softened in response to endogenous and exogenous ethylene/propylene. DNA-seq analysis showed that tandem endo-polygalacturonase (<italic>endoPG</italic>) genes located at <italic>melting flesh (M)</italic> locus, <italic>Pp-endoPGM</italic> (<italic>PGM</italic>), and <italic>Pp-endoPGF</italic> (<italic>PGF</italic>), were deleted in DJ. The <italic>endoPG</italic> genes at <italic>M</italic> locus are known to control flesh texture of peach fruit, and it was suggested that the non-softening property of DJ is due to the lack of <italic>endoPG</italic> genes. On the other hand, TH possessed an unidentified <italic>M</italic> haplotype that is involved in determination of MF phenotype. Structural identification of the unknown <italic>M</italic> haplotype, designated as <italic>M</italic>⁰, through comparison with previously reported <italic>M</italic> haplotypes revealed distinct differences between <italic>PGM</italic> on <italic>M</italic>⁰ haplotype (<italic>PGM-M⁰</italic>) and <italic>PGM</italic> on other haplotypes (<italic>PGM-M¹</italic>). Peach <italic>M</italic> haplotypes were classified into four main haplotypes: <italic>M</italic>⁰ with <italic>PGM-M⁰</italic>; <italic>M</italic>¹ with both <italic>PGM-M¹</italic> and <italic>PGF</italic>; <italic>M</italic>² with <italic>PGM-M¹</italic>; and <italic>M</italic>³ lacking both <italic>PGM</italic> and <italic>PGF</italic>. Re-evaluation of <italic>M</italic> locus in association with MF/non-melting flesh (NMF) phenotypes in more than 400 accessions by using whole genome shotgun sequencing data on database and/or by PCR genotyping demonstrated that <italic>M</italic>⁰ haplotype was the common haplotype in MF accessions, and <italic>M</italic>⁰ and <italic>M</italic>¹ haplotypes were dominant over <italic>M</italic>² and <italic>M</italic>³ haplotypes and co-dominantly determined the MF trait. It was also assumed on the basis of structural comparison of <italic>M</italic> haplotypes among <italic>Prunus</italic> species that the ancestral haplotype of <italic>M</italic>⁰ diverged from those of the other haplotypes before the speciation of <italic>Prunus persica</italic>.