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Cotton fiber is an extremely elongated single cell that is considered as an ideal system for studying the mechanisms controlling plant cell elongation. In this study, suppression subtractive hybridization (SSH) between RNA from leaves and fibers of cotton plant was conducted to identify genes that are specifically or preferentially expressed in fiber cells. Screening the resulting SSH library by reverse Northern analysis identified a total of 180 differentially expressed cDNA fragments. Sequencing determination and database analysis revealed 64 non-redundant cDNA clones, of which, 25 code for unknown-function proteins. Among these cDNAs, four were found to encode for proteins that showed high homology to calcium signaling components including calmodulin (CaM), glutamate decarboxylase (GAD) and calcineurin B-like (CBL) protein-interacting protein kinases (CIPKs). RT-PCR analysis indicated that the transcripts of these genes were accumulated predominantly in elongating fiber cells. Moreover, the expression level of these genes was significantly reduced in the li (ligon-lintless) mutant fibers as compared to the wild-type control. One of the two CIPKs, designated as GhCIPK1, was further characterized in this study. Structural analysis showed that GhCIPK1 contained the characteristic domains of CIPK proteins and was highly expressed in the elongating phase in developing fiber, and in vitro assay demonstrated that the gene product was a functional protein kinase. Our results suggest that calcium-mediated signal transduction may play an important role in cotton fiber elongation.