Phased small interfering RNA (phasiRNA) generating loci (briefly as PHAS) in plants are a novel class of genes that are normally regulated by microRNAs (miRNAs). Similar to miRNAs, phasiRNAs encoded by PHAS play important regulatory roles by targeting protein coding transcripts in plant species. We performed a genome-wide discovery of PHAS loci in Chinese sacred lotus and identified a total of 106 PHAS loci. Of these, 47 loci generate 21 nucleotide (nt) phasiRNAs and 59 loci generate 24nt phasiRNAs, respectively. We have also identified a new TAS3 and two TAS4 loci in the lotus genome. Our results show that some of the nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance proteins and MYB transcription factors generate phasiRNAs. Furthermore, our results suggest that some LSU-rRNAs can derive phasiRNAs, which is potentially resulted from crosstalk between small RNA biogenesis pathways that are employed to process rRNAs and PHAS loci, respectively. Some of the identified phasiRNAs have trans-targets with less than 4 mismatches, suggesting that the identified PHAS are involved in many different pathways. Finally, the discovery of 24nt in lotus suggests that there are 24nt PHAS in dicots.