Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.