Silicoaluminophosphates with the ATO structure have been synthesized using two types of silicon source (metakaolin and silica sol). To determine the composition, morphology, and acid properties, SAPO-31 samples have been characterized by various methods. It has been found that the samples synthesized using different silica sources have very different properties. Samples of SAPO-31 synthesized with metakaolin have a higher acidity and are more active in the catalytic hydroisomerization of n-decane as compared with their counterparts prepared with silica sol. The difference in the effect of the type of silicon source has been explained by morphological features of silica particles formed during the dissolution of silicon source (spherical particles of a similar to 10 nm size in the case of silica sol and nanoplates of a similar to 1 nm size in the case of metakaolin). On the basis of data on the enhancement of acidic properties in the SAPO-31 samples with an increase in silicon concentration therein, it has been doubted that the SM3 mechanism of incorporation of Si atoms into the aluminophosphate ATO framework really operates (in any of its form). It has been shown that the SM2 mechanism alone operates instead, involving the independent formation of regions with an aluminosilicate composition.