I'm trying to learn how to write geopackage SQL queries so that the r tree index is used, but I can't seem to find any good information. I'm just trying to write a simple query in the qgis db manager like so:

SELECT pts.* 
FROM pts, polys, 
WHERE ST_WITHIN(pts.geom,polys.geom)

it takes an extremely long time, but running the same query in qgis using the select by location tool is nearly instant. I figure that the select by location tool must be using a spatial index, while the query is not. I know that spatial indexes must be explicitly included in a geopackage query, but I can not seem to find out how to do so. how do I rewrite this query to use the rtree spatial index?

I am forced by work to use QGIS version 3.12.3 to create and access my geopackages,although running gdalinfo --version in the OSGeo4W shell indicates I am using GDAL 3.0.4

  • 2
    Did you try do run SELECT CreateSpatialIndex('table_name', 'geom_column_name')? in the DB Manager then your query again to see if speedup? See also medium.com/@wherelytics/… to use index in your SQL query
    – ThomasG77
    Jul 13, 2021 at 14:50
  • I did, no dice. I think it needs to have the spatial index explicitly called to work. in spatialite, for example, the following query runs quite fast. SELECT points.* FROM polys, points WHERE ST_Within(points.geometry, polys.geometry) = 1 AND points.ROWID IN ( SELECT ROWID FROM SpatialIndex WHERE f_table_name = 'points' AND search_frame = polys.geometry ); however this syntax does not seem to work in geopackages
    – Alex
    Jul 13, 2021 at 18:22
  • You can find SQL examples with a subquery and JOIN from erouault.blogspot.com/2017/03/…. I am not sure if the finding about JOIN being faster is true for all use cases.
    – user30184
    Jul 14, 2021 at 21:39

1 Answer 1


GeoPackage is using "rtree" as a name of the spatial index. The basic usage with subquery is

SELECT * FROM the_table WHERE fid IN 
       (SELECT id FROM the_rtree WHERE 
        xmin <= bbox_xmax AND xmax >= bbox_xmin AND
        ymin <= bboy_ymay AND ymay >= bboy_ymin)
  • I'd add that the convention for Rtrees in Geopackages seems to be rtree_thislayer_geom for layer thislayer, and coordinates are labelled as miny, maxy, minx and maxx Nov 10, 2022 at 20:19

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