||Esophageal squamous cell carcinomas (ESCC) is a leading cause of cancer death, especially in eastern Asian area. Mapping the transcriptional landscape such as isoforms, fusion transcripts as well as long noncoding RNAs, have played a central role to understand the regulating mechanism during malignant processes. However, canonical methods such as microarrays and short-read RNA-seq are difficult to define the entire polyadenylated RNA molecule structure. Here we use PacBio SMRT platform to generate high-quality long reads, and to survey the full length RNA molecules in five esophageal squamous cell lines. Compared with the recent annotations of human transcriptome (Ensemble 38 release 91), SMRT data reveal many unannotated transcripts and isoform structures in each cell line, indicating the diverse alternative splicing patterns and transcribed RNA molecules. Based on SMRT long reads, many lncRNAs are also predicted with high confidence by multiple analyzing tools. Utilizing vigorous heuristics criteria, we also detect multiple transcript fusions, which are not documented in current gene fusion database or readily identified from RNA-seq short reads. Overall, our study provides a global view of the full length transcriptome with long-read single molecule sequencing, and elucidates a more comprehensive assessment of the true complexity in esophageal cells.