The effect of spongean alkaloids aaptamine (1), isoaaptamine (2), 9-demethylaaptamine (3), aaptanone (4), N-demethylaaptanone (5), and semisynthetic 4-N-methylaaptanone (6) was studied on the growth of seedlings roots of soy {Glycine max (L.) Merr.}, maize (Zea mays L.), wheat (Triticum aestivum L.), buckwheat (Fagopyrum esculentum Moench), and barley (Hordeum vulgare L.). It was shown that a stimulatory effect depends on the chemical structure of the compounds and species of crop plants. The structural motif of aaptamines 1–3 is essential for a stimulating activity on the growth of seedling roots of soy, maize, and wheat. The oxygenated 1,6-naphthyridine core of aaptanones 5 and 6 is important for their growth stimulating activity on barley roots.