The results of palynological and micropaleontological studies of the Upper Cretaceous–Cenozoic strata penetrated by Boreholes 23 and 19 of the Aleiskaya area (Altai krai) are presented. The obtained data allowed us to substantiate the age of the deposits, make suggestions concerning their depositional environment, and to clarify the subdivision of geological section into formations. Two palynological assemblages were recognized in the Cretaceous part of the Borehole 23 section: the first one characterizes the Len’ki Formation and is dated as Cenomanian–Turonian; the second one is recognized in the Upper Sym Subformation and is dated as Maastrichtian. The Upper Cretaceous sequence is overlain by the terrestrial Ostrovnoe Formation (Paleogene). In Boreholes 19 and 23, this formation contains presumably Late Paleocene–Early Eocene and Middle Eocene spore and pollen spectra, respectively. Palynological data substantiate the Late Miocene age of sedimentary strata in the upper part of the geological section of Borehole 23 and their belonging to the Pavlodar Formation. The structure of the palynological assemblages, the specific features of the macerate, and the absence of foraminifers indicate the continental genesis of the Upper Cretaceous–Paleogene sedimentary deposits in the southern part of the Kulunda Depression in Altai krai.