diff --git a/etc/pyenv.d/which/whence.bash b/etc/pyenv.d/which/whence.bash
index 11a84fe..59855e5 100755
--- a/etc/pyenv.d/which/whence.bash
+++ b/etc/pyenv.d/which/whence.bash
@@ -1,8 +1,15 @@
 if [ -n "$PYENV_COMMAND" ] && [ ! -x "$PYENV_COMMAND_PATH" ]; then
   versions=($(pyenv-whence "${PYENV_COMMAND}" 2>/dev/null || true))
   if [ -n "${versions}" ]; then
-    if [ "${#versions[@]}" -gt 1 ]; then
-      echo "pyenv-implicit: found multiple ${PYENV_COMMAND} in pyenv. Use version ${versions[0]}." 1>&2
+    if [ "${#versions[@]}" -gt 2 ]; then
+      echo "pyenv-implicit1: found multiple ${PYENV_COMMAND} in pyenv. Use version ${versions[0]}." 1>&2
+    elif [ "${#versions[@]}" -gt 1 ]; then
+      pattern0="[1-9][0-9]*\.[0-9]*\.[0-9]*/envs/${versions[0]}$"
+      pattern1="[1-9][0-9]*\.[0-9]*\.[0-9]*/envs/${versions[1]}$"
+      # Commands in virtualenvs are always listed twice.  Ignore this warning if both versions are the same virtualenv
+      if ! [[ "${versions[0]}" =~ $pattern1 ]] && ! [[ "${versions[1]}" =~ $pattern0 ]]; then
+        echo "pyenv-implicit2: found multiple ${PYENV_COMMAND} in pyenv. Use version ${versions[0]}." 1>&2
+      fi
     fi
     PYENV_COMMAND_PATH="${PYENV_ROOT}/versions/${versions[0]}/bin/${PYENV_COMMAND}"
   fi