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Background: Poplar seed hair is an environmental annoyance in northern China due to its abundance and widespread airborne distribution after maturation. The morphogenesis and molecular mechanisms of its development are not well understood, and little attention has been focused on the dynamics of its development. To better understand the mechanism of poplar seed hair development, paraffin sections were used to examine the initiation and elongation of poplar seed hairs. RNA-seq technology was also employed to provide a comprehensive overview of transcriptional changes that occur during seed hair development., Results: The placenta at the base of ovary, was identified as the origin of seed hair development, which is in sharp contrast to cotton fibers that originate from epidermal cells of the seed coat. An enlarged cell nucleus in seed hair cells was also observed, which was supported by our gene ontology enrichment analysis. The significant enriched GO term of "endoreduplication" indicated that cycles of endoreduplication, bypassing normal mitosis, is the underlying mechanisms for the maintenance of the uni-cellular structure of seed hairs. By analyzing global changes in the transcriptome, many genes regulating cell cycle, cell elongation, cell well modification were identified. Additionally, in an analysis of differential expression, cellulose synthesis and cell wall biosynthesis-related biological processes were enriched, indicating that this component of fiber structure in poplar seed hairs is consistent with what is found in cotton fibers. Differentially expressed transcription factors exhibited a stage-specific up-regulation. A dramatic down-regulation was also revealed during the mid-to-late stage of poplar seed hair development, which may point to novel mechanisms regulating cell fate determination and cell elongation., Conclusions: This study revealed the initiation site of poplar seed hairs and also provided a comprehensive overview of transcriptome dynamics during the process of seed hair development. The high level of resolution on dynamic changes in the transcriptome provided in this study may serve as a valuable resource for developing a more complete understanding of this important biological process.