Btree and Rtree are two basic index structures; many different variants of them are proposed after them. Different variants are used in specific application for the performance optimization. In this paper different variants of Btree and Rtree are discussed and compared. Index structures are different in terms of structure, query support, data type support and application. Index structures are discussed first. Btree and its variants are discussed and them Rtree and its variants are discussed. Some structures example is also shown for the more clear idea. Then comparison is made between all structure with respect to complexity, query type support, data type support and application.