Spatial indexing has been one of the active focus areas in recent database research. Several variants of Quadtree and R-tree indexes have been proposed in database literature. In this paper, we first describe briefly our implementation of Quadtree and R-tree index structures and related optimizations in Oracle Spatial. We then examine the relative merits of the two structures as implemented in Oracle Spatial and compare their performance for different types of queries and other operations. Finally, we summarize our experiences with these different structures in indexing large GIS datasets in Oracle Spatial.