Papaya seeds presents irregular and slow germination. In this sense, the evaluation of the internal morphology of the seeds may be viable and complementary in evaluating the physiological quality of seed. The objective of this study was to evaluate the morphological and physiological quality of papaya seeds extracted at different ripeness stages of the fruit and the position inside of the fruit. Papaya fruits were harvested at maturity stage 1 and the seeds extracted in stages 1, 3, 5 and full maturation. The fruits were cut into three portions of equal size. Seeds of the central portion and extremities were extracted separately. Were determined: seed germination (%), dormant seeds (%), accelerated aging, X-ray test and seedling length. A randomized design factorial was used with four replications. Data were subjected to analysis of variance and treatment means were compared by Tukey test at 5% probability. The results demonstrated that the post-harvest maturity of fruits improves the physiological quality of papaya seeds, promoting a reduction in the number of dormant and non-viable seeds. High physiological quality seeds is obtained from the central portion of fruits at fifth and final maturation stages, corresponding from 75% to 100% of maturation, respectively. The X-ray test proved to be adequate to evaluate the morphological quality of papaya seed, allowing distinguish between empty seeds and seed with normal embryo within a sample.