The Amazon region of Peru is one of the regions with the greatest potential in the production of natural resources in the country, including native papayas. The objective of this research was to conduct a comparative study of the physicochemical characteristics and shelf life of native papayas such as Papayita del Monte (Carica pubescens Lenné & K. Koch) and babaco (Carica pentagona Heilborn) dehydrated by lyophilization. The physicochemical characteristics as well as the biometric values of both varieties were determined. Additionally, the total polyphenol content was quantified by the spectrophotometric method, the antioxidant capacity by the DPPH method and the shelf life of the freeze dried papayite and tobacco pulps, which were bagged, were determined mathematically. The results indicate that in relation to biometric analyzes such as weight, length and diameter, between papayite and babaco if there is a significant statistical difference (p-value = 0.0001). The comparison of the physicochemical characteristics between papayita and babaco pulps statistically existed a significant difference between them. The comparison between the yields of lyophilized pulps of papayite and babaco was determined a difference of 0.12. In the comparison of the total phenolic content between fresh pulps and lyophilized pulps if there was a significant difference, between papayite and babaco respectively, where it was determined that lyophilized products have a higher total phenolic content, than fresh pulp products. Also, in the antioxidant capacity if there are significant differences between fresh and lyophilized pulps between papayite and babaco. It was also determined that the lyophilized papayite pulp has a higher antioxidant capacity than the lyophilized pulp of the babaco. [ABSTRACT FROM AUTHOR]