Two novel medium pore cobalt-substituted aluminophosphate molecular sieves CoAPO-41 and CoAPSO-41 have been synthesized hydrothermally using di-n-propylamine as the organic template. These materials have been characterized by various physical methods including XRD, TGA, SEM, electron microprobe analysis, Al-27, Si-29, and P-31 MAS NMR, UV-visible, and ESR spectroscopies. Substitution of cobalt into the framework has been established. Cobalt in CoAPO/CoAPSO-41 after calcination in O-2 and subsequent dehydration and H-2 treatment at high temperature activates molecular oxygen by forming a peroxocobalt adduct Co-O-O-.. The peroxo species is unstable at temperatures above 573 K. Adsorption of molecules such as D2O, ND3, CH3OD, and CO on CoAPO/CoAPSO-41 materials after calcination, dehydration, and high-temperature hydrogen treatment forms complexes with Co(II) from the framework as revealed by ESR measurements at 4.5 and 77 K.