Soil microbial abundance, which is related to soil characteristics and process rates, is an early indicator of changes in soil health and quality. However, microbial functional groups in permafrost peatland soils have rarely been studied. These soils are important C and N stores and possibly vulnerable to climate warming. We randomly gathered surface soils (0-15 cm and 15-30 cm soil layers) from 10 peatlands in sporadic island, discontinuous island, and continuous permafrost regions in Northeast China. The aim was to clarify the soil microbial abundance distribution in different types of permafrost peatlands. Results revealed different effects of permafrost types on different soil C- and N-cycling microbial abundances in peatlands. The bacteria, amoA, and nirK gene abundances in the two soil layers were the highest in discontinuous island permafrost peatlands. Soil mcrA and pmoA gene abundances in 0-15 cm soil were high in continuous and discontinuous island permafrost peatlands, respectively. The amoA gene abundance in both soil layers and nirS gene abundance in 15-30 cm soil were high in discontinuous island permafrost peatlands. The average nirK gene abundance in both soil layers was in the order: discontinuous island permafrost peatlands > continuous permafrost peatlands > sporadic island permafrost peatlands. No significant differences in archaeal abundance were observed in both soil layers among the different types of permafrost peatlands. Moreover, 42.5%, 15.9%, and 15.3% of the variation in soil microbial abundances could be explained by soil ammonia-N, pH, and total C, respectively. Our results imply that soil microbial abundance can be utilized as effective soil N availability, C pool, and pH indicators in permafrost peatlands.