The aim of this paper is to introduce nine types of rough Pythagorean fuzzy sets in UP-algebras and nine types of rough sets in UP-algebras. Then we study relation of these rough Pythagorean fuzzy sets and new types of Pythagorean fuzzy UPfilter under equivalence (congruence) relation. Moreover, we will also discuss t-level subsets of rough Pythagorean fuzzy sets in UP-algebras to study the relationships between rough Pythagorean fuzzy sets and rough sets in UP-algebras which we defined them above. Finally, we discuss the concept of homomorphisms between IUP-algebras and also study the direct and inverse images of four special subsets.