Long noncoding RNAs(lnc RNAs)play important roles in various biological regulatory processes in yeast,mammals,and plants.However,no systematic identification of lnc RNAs has been reported in Gossypium arboreum.In this study,the strand-specific RNA sequencing(ss RNA-seq)of samples from cotton fibers and leaves was performed,and lnc RNAs involved in fiber initiation and elongation processes were systematically identified and analyzed.We identified 5,996 lnc RNAs,of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs(linc RNAs)and natural antisense transcripts(lnc NAT),respectively.Linc RNAs and lnc NATs are similar in many aspects,but have some differences in exon number,exon length,and transcript length.Expression analysis revealed that 51.9%of linc RNAs and 54.5%of lnc NATs transcripts were preferentially expressed at one stage of fiber development,and were significantly highly expressed than protein-coding transcripts(21.7%).During the fiber and rapid elongation stages,rapid and dynamic changes in lnc RNAs may contribute to fiber development in cotton.This work describes a set of lnc RNAs that are involved in fiber development.The characterization and expression analysis of lnc RNAs will facilitate future studies on their roles in fiber development in cotton. Long noncoding RNAs (lnc RNAs) play important roles in various biological regulatory processes in yeast, mammals, and plants. Host, no systematic identification of lnc RNAs has been reported in Gossypium arboreum. In this study, the strand-specific RNA sequencing RNA-seq) of samples from cotton fibers and leaves was performed, and lnc RNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lnc RNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs ( linc RNAs) and natural antisense transcripts (lnc NAT), respectively.Linc RNAs and lnc NATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of linc RNAs and 54.5% of lnc NATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding transcripts (21.7%). During the fiber and rapid elongation stages, rapid and dynamic changes in lnc RNAs may contribute to fiber development in cotton. This work describes a set of lnc RNAs that are involved in fiber development. characterization and expression analysis of lnc RNAs will facilitate future studies on their roles in fiber development in cotton.