Calcineurin B-like-interacting protein kinase (CIPKs) was one kind of serine/threonine kinases, playing crucial roles in abiotic stresses and hormones signal transduction pathways. Based on soybean genome database, a total of 52 CIPK genes were identified from soybean. Multiple alignments showed that all soybean CIPK proteins had the conserved regions which were composed of an N-terminal kinase domain, a junction region and a C-terminal regulatory domain. Phylogenetic analysis of CIPKs form soybean, Arabidopsis and rice revealed that all CIPKs were classified into four subfamilies and each subfamily was composed of homologous CIPKs from these three species. The classification of CIPKs from soybean was consistent with Arabidopsis and rice, which implied that the differentiation of CIPK genes occurred before the evolution of plant species. Promoter sequences analysis suggested that most GmCIPKs had stress and hormone related cis-acting elements in their promoter regions. Tissues expression analysis revealed that each GmCIPK had different expression pattern in different tissues. Furthermore, 14 GmCIPKs with relatively higher transcript level in different tissues were selected to investigate their transcriptional response to various stimuli by real-time PCR. The results showed the comprehensive responses of the tested GmCIPKs to heat, drought, salt stressors and ABA, ACC, SA, MeJA signaling. By BLASTP analysis, 17 orthologous GmCIPKs involved in CIPK interaction networks were identified between Arabidopsis and soybean. The findings of this study will provide a foundation for the functional characterization of the GmCIPK genes in vegetable soybean.