diff --git a/README.md b/README.md
index dd3573e..bc47228 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 
 ![Alt text](funannotate-logo.png?raw=true "Funannotate")
 
-funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at [http://funannotate.readthedocs.io](http://funannotate.readthedocs.io)
+funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at <https://funannotate.readthedocs.io>. Since 2025, it has been superseded by funannotate2, see <https://github.com/nextgenusfs/funannotate2> and <https://funannotate2.readthedocs.io>.
 
 #### Quickest start Docker:
 
diff --git a/docs/index.rst b/docs/index.rst
index 70281f4..9d08864 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -26,7 +26,7 @@ Funannotate is a genome prediction, annotation, and comparison software package.
 
 Funannotate is also a lightweight comparative genomics platform. Genomes that have had functional annotation added via the :code:`funannotate annotate` command can be run through the :code:`funannotate compare` script that outputs html based whole genome comparisons. The software can run orthologous clustering, construct whole-genome phylogenies, run Gene Ontology enrichment analysis, as well as calculate dN/dS ratios for orthologous clusters under positive selection.
 
-
+Here we are describing funannotate version *one*, which has been superceeded since 2025 by version *two*, see `funannotate2 <https://funannotate2.readthedocs.io/>`__.
 
 * :ref:`install`
 * :ref:`prepare`
diff --git a/docs/install.rst b/docs/install.rst
index 2793c99..fa9886e 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -11,7 +11,9 @@ Installation
 
 Funannotate has a lot of dependencies and therefore installation is the most difficult part
 of executing the pipeline. The  funannotate pipeline is written in python and can be installed
-with pip, i.e. `pip install funannotate`.  You can see a list of :ref:`dependencies`,
+with pip, i.e. `pip install funannotate`.  You can see a list of :ref:`dependencies`.
+
+Note here we are describing how to install funannotate version *one*. This was superceeded in 2025 by version *two* where a major goal was to reduce the dependencies to simplify installation, see `funannotate2 <https://funannotate2.readthedocs.io/>`__.
 
 Quickest start Docker:
 ----------------------