In the present work, a plausible host candidate is provided for the separation of 3-methylpyridine (3MP) from 4-methylpyridine (4MP), isomers that are extremely difficult to separate by conventional means. Host compound N,N′-bis(9-phenyl-9-xanthenyl)ethylenediamine (H2), when recrystallized from an equimolar mixture of 3MP and 4MP, contained 91.6% 3MP, a significantly improved outcome compared with the alternate host compound N,N′-bis(9-phenyl-9-thioxanthenyl)ethylenediamine (H1) which only enclathrated 70% of this isomer in the same experimental conditions. Single crystal diffraction and thermoanalytical experiments were conducted in order to investigate this preference for 3MP by considering both host⋯guest interactions and relative complex stabilities. Many of the guest components in 3(H2)·5(3MP)·0.268(O) experienced at least one other short contact measuring less than the sum of the van der Waals radii of the involved atoms, an observation that may explain the selectivity of H2 for this guest since this was not the case in complexes containing PYR and 4MP. Results from the thermal analyses were less informative.