In this study, five U2 small nuclear (sn)RNA variants were detected in the posterior silk gland of the Bombyx mori Nistari strain, one of which represents a novel U2 isoform not previously identified in other strains of this species. Following glycerol gradient ultracentrifugation of B. mori silk gland whole cell lysate, the newly isolated variant, U2α, was detected at a greater frequency in total cell lysate than in a high density glycerol gradient fraction rich in spliceosomal complexes. Conversely, previously identified isoforms U2A, U2B, U2D and U2N are abundant in the fraction containing high molecular weight spliceosomal complexes, possibly indicating their greater involvement in splicing. As expected, western blot and semi-quantitative reverse transcription-polymerase chain reaction experiments indicate high levels of specific serine and arginine rich (SR) proteins and total U2 snRNA (all variants included) in the fraction enriched in spliceosomes. Free energy values for each U2 isoform, as well as their individual stem-loops, were estimated to determine their structural stability. Due to the essential role of U2 in the transesterification reactions, it is possible that these isoforms may modulate splicing through differential incorporation into the spliceosome. © 2009 The Entomological Society of Korea and Blackwell Publishing Asia Pty Ltd.