PhoH is a host-derived auxiliary metabolic gene that can be used as a new biomarker for surveying phage diversity in marine and paddy waters. However, the applicability of this gene in other environments has not been addressed. In this paper, we surveyed the phoH gene in four wetland sediments in northeast China. DNA was extracted directly from sediments and used for PCR amplification with the degenerate primers vPhoHf and vPhoHr. In total, 44 and 58 phoH sequences were identified as belonging to bacteria and phages, respectively, suggesting that this primer set is not highly specific to the phage phoH gene. A BLASTp search showed that the 58 phage phoH sequences had the highest identity to the known viral sequences, ranging from 48% to 100%. Phylogenetic analysis showed that all phage sequences from wetlands distributed into the previously designated Groups 2, 3, 4 and 6. In addition, two new subgroups, Groups 2c and 4c, which contained sequences exclusively from wetlands, were detected in this study. Nonmetric multidimensional scaling analysis showed that the phage phoH assemblage from a coastal wetland was similar to that in marine environments, while the phage phoH assemblage from a lake wetland was similar to that in paddy waters. These findings indicated that different types of wetlands had distinct phage phoH compositions.