The title nonplanar electron acceptor (1) fused with a selenadiazole ring selectively forms a crystalline charge-transfer complex (CT crystal) with 2,6-dimethylnaphthalene (2,6-DMN). On the other hand, the sulfur analogue (2) has less recognition ability and forms CT crystals with both 2,6-and 2,7-DMN. X-ray analyses of 1, 2, and their CT crystals revealed that the Se ••• N chalcogen bond (ChB) in 1 is strong enough to determine the crystal packing with the formation of a cavity suitable for 2,6-DMN. On the contrary, ChB through S ••• N contact in 2 competes with other weak interactions such as a C-H ••• N hydrogen bond. The stronger ChB involving Se is the key for 1 to separate 2,6-DMN (>97 wt%) from a complex isomer mixture containing ca. 10 wt% each of 2,6and 2,7-DMN by a simple, efficient and straightforward mixingfiltration-heating process.