Papaya is a model system for the study of sex chromosome evolution in plants. However, the cytological structures of the papaya chromosomes remain largely unknown and chromosomal features have not been linked with any genetic or genomic data. We constructed a cytogenetic map of the papaya sex chromosome (chromosome 1) by hybridizing 16 microsatellite markers and 2 cytological feature-associated markers on pachytene chromosomes using fluorescence in situ hybridization (FISH). Except for three markers, the order of the markers was concordant to that of marker loci along the linkage map. This discrepancy was likely caused by skewed segregation in the highly heterochromatic or centromeric regions. The papaya sex chromosome is largely euchromatic, its heterochromatin spans about 15 % of the Y chromosome and is mostly restricted to the centromeric and pericentromeric regions. Analysis of the recombination frequency along the papaya sex chromosome revealed a complete suppression of recombination in the centromere and pericentromere region and 60 % higher recombination rate in the long arm than in the short arm. The uneven distribution of recombination events might be caused by differences in sequence composition. Sequence analysis of 18 scaffolds in total length of 15 Mb revealed higher gene density towards the telomeres and lower gene density towards the centromere, and a relatively higher gene density in the long arm than in the short arm. In an opposite trend, the centromeric and pericentromeric region contained the highest repetitive sequences and the long arm showed the lowest repetitive sequences. This cytogenetic map provides essential information for evolutionary study of sex chromosomes in Caricaceae and will facilitate the analysis of papaya sex chromosomes.