The flora of the sanctuary is less well studied than the flora of Kronotsky Nature Reserve. In all, 438 species in 212 genera and 109 families have been identified here. Four species and one genus are invasives. The species composition of the sanctuary and Kronotsky Reserve differs significantly for a number of reasons. The area of Kronotsky is four-and-half-times larger than the sanctuary, thus Kronotsky has more natural conditions and ecotypes, a higher continental gradient, and a more expressed oceanic climate influence. Also biogeographic factors come into play. Most of the sanctuary is characterized as the Southern sub-region type, but Lopatka Peninsula is considered as part of the Northern Kuril sub-region. Infact, flora types transition gradually throughout the entire sanctuary from poor island-oceanic flora to the more abundant sub-continental flora of Kamchatka. Thirty species in the sanctuary have never been observed in Kronotsky, some of which are generally found on the Kuril Islands and in other parts of southern Kamchatka, including Rieder’s saw-wort (Saussurea riederi), a species of Venus’ looking-glass (Perаcarpa circaeoides), Rieder’s globe flower (Trollius riederanus), Chamisso’s bellflower (Campanula chamissonis), goldenbaner (Thermopsis lupinoides), Steller’s Veronica (Veronica stellerti),among others. Seven species in the sanctuary are considered regionally rare and are protected.
The plant community of the sanctuary consists of 23 formations, 9 vegetation types, and 46 associations. Low woodlands of shrub alder, Siberian dwarf pine, and mountain tundra cover the majority of the terrain of the reserve. Prevalence of Erman birch stands, dwarf alder and pine forests, and mountain tundra depends on altitude. Marshes, floodplain forests, and meadows are also found here. Plant diversity in the South Kamchatka Sanctuary is less than that of Kronotsky Reserve, for example, there are no fir or larch forests or Chosenia brush.