diff --git a/dev-python/rtree/Manifest b/dev-python/rtree/Manifest
index fd47b2299158b..97f14c5b580a1 100644
--- a/dev-python/rtree/Manifest
+++ b/dev-python/rtree/Manifest
@@ -1,2 +1 @@
-DIST rtree-1.3.0.tar.gz 48190 BLAKE2B 1a9ed3617ca14e3a88e5800e871e3d3edd58bc31d5dcad3c30a4a3a51b44678beacfddc1c72cbd984139e8e9acfffda45cc478857dacba5b44e7775f29ef890f SHA512 28810b769d90914e5aea9ea0b7f27b946c8d19495965696624d4fdd94c6ad462eb5ce7004d2c41e017d14a69bc913f43fdcef5293abe8504b66d8dcd5f4955a2
 DIST rtree-1.4.0.tar.gz 50789 BLAKE2B b3897a0c5332843c4c938a4ff494d17f006e05891bb6af70cae19ac323aec21bb5f42fdb3066c2a26007dbcd171258566f5ec67fba7ad9945f30c8929a005d17 SHA512 8306d519169f067d6c97adeb7a18d5053c192437b8a2b7288c2bfb379d2bdd885ac3b400d37ecdad224d1aaee542f6b9f50567baae5a8b02a23419f1da562b5e
diff --git a/dev-python/rtree/rtree-1.3.0.ebuild b/dev-python/rtree/rtree-1.3.0.ebuild
deleted file mode 100644
index 743c1eb584160..0000000000000
--- a/dev-python/rtree/rtree-1.3.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..13} )
-DISTUTILS_USE_PEP517=setuptools
-PYPI_PN=${PN^}
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="R-Tree spatial index for Python GIS"
-HOMEPAGE="
-	https://rtree.readthedocs.io/
-	https://github.com/Toblerity/rtree/
-	https://pypi.org/project/Rtree/
-"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="amd64 arm64 ~x86"
-
-RDEPEND="
-	sci-libs/libspatialindex
-	dev-python/typing-extensions[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
-	test? (
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-"
-
-distutils_enable_sphinx docs/source \
-	dev-python/sphinx-issues
-distutils_enable_tests pytest