We have analysed the angular clustering of X-ray selected active galactic nuclei (AGN) in different flux-limited sub-samples of the Chandra Deep Field North (CDF-N) and South (CDF-S) surveys. We find a strong dependence of the clustering strength on the sub-sample flux-limit, a fact which explains most of the disparate clustering results of different XMM and Chandra surveys. Using Limber’s equation, we find that the inverted CDF-N and CDF-S spatial clustering lengths are consistent with direct spatial clustering measures found in the literature, while at higher flux-limits the clustering length increases considerably; for example, at fx, limit ∼10 ¯¹⁵ˉ erg s¯¹ cm¯² we obtain r₀ ≃ 17 ± 5 axxnd 18 ± 3 h−1 Mpc, for the CDF-N and CDF-S, respectively. We show that the observed flux-limit clustering trend hints towards an X-ray luminosity dependent clustering of X-ray selected, z ∼ 1, AGNs.