We have analyzed the angular clustering of X-ray-selected active galactic nuclei (AGNs) in different flux-limited subsamples of the Chandra Deep Field North (CDF-N) and South (CDF-S) surveys. We find a strong dependence of the clustering strength on the subsample flux limit, a fact that 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 ~ 10−15 ergs s−1 cm−2, we obtain r0sime 17 ± 5 and 18 ± 3 h−1 Mpc for the CDF-N and CDF-S, respectively. We show that the observed flux limit clustering trend hints toward an X-ray luminosity dependent clustering of X-ray-selected, z ~ 1, AGNs.