The plant low temperature tolerance mechanisms have been studied in the Arabidopsis, tomato, Solanum commersonii, Solanum tuberosum, Chorispora bungeana, and Chinese cabbage at the transcriptional level. Some genome-wide works to identify cold-regulated genes, but no comprehensive research of the Solanum lycopersicoides transcriptome under low temperature stress have been performed. S. lycopersicoides is more freeze-tolerant than the cultivated tomato. We analyzed the low temperature transcriptomes and small RNA fractions of S. lycopersicoides leaf tissue using an Illumina platform for high-throughput RNA sequencing (RNA-seq). There were 59,286 unigenes obtained using de novo assembly, and 2052 down-regulated and 2409 up-regulated unigenes were identified in response to chilling. The expression of six cold-regulated genes was confirmed by qPCR. Some biological processes were showed, by gene ontology term enrichment analysis of the cold-regulated genes, including 'response to stimulus', 'signaling', and 'cell killing' in the response of S. lycopersicoides to chilling. In addition, we identified a total of 952 novel miRNA candidates that may regulate relevant target genes. Our data indicated that certain miRNAs (e.g., sly-miR156a, sly-miR397, and unconservative_SL2.50ch00_21686) play roles in response to low temperature stress. Sequencing of mRNAs and miRNAs revealed new genes and allowed us to have new assumptions for a low temperature tolerance mechanism. (C) 2015 Elsevier Inc. All rights reserved.