The "proto-spotted eagle" probably lived in the general region of Afghanistan, being split into a northern and a southern lineage when both glaciers and deserts advanced in Central Asia as the last ice age began.

The northern lineage subsequently separated into the eastern (greater) and western (lesser) species of today, probably around the Pliocene-Pleistocene boundary not quite 2 million years ago.

[8] The lesser spotted eagle breeds in Central and Eastern Europe and southeastward to Turkey and Armenia;[9] and winters in Africa.

[12] The lesser spotted eagle uses regularly spaced territories consistently between years in the north-western part of its distribution.

Synchronous variation in breeding success across the region indicates that the eagles are instead influenced by large-scale factors such as fluctuations in climate or prey availability.