Rising ambient temperature is crucial for plants for the timely activation of several defense mechanisms before the damage occurs due to heat. During heat stress, plants undergo several mechanisms of regulation at the molecular level to circumvent damage due to stress and to prevent cell death. Alternative splicing (AS) is one type of a posttranscriptional regulatory mechanism that also produces a tremendous amount of transcriptome and proteome variation. A previous study conducted in our lab on the heat stress response of six Arabidopsis thaliana and five diverse species of Boechera (Brassicaceae), found that A. thaliana is highly heat sensitive, while B. depauperata is highly heat resistant. To determine whether AS affects the heat stress responses of A. thaliana and B. depauperata, I investigated splicing patterns of genes expressed in roots of 7-10 days old seedlings at temperatures ranging from 22°C to 43°C. RNAseq was used to sequence transcript variants and several already available bioinformatic tools and specially written codes were utilized to identify splice junctions. I found that approximately ~46% of introncontaining genes were alternatively spliced and between those ~10% were deferentially alternatively spliced in A. thaliana. Analysis of the functional categories in both plants revealed that genes with aberrant splicing were involved in transcription factor regulation (positive/negative) of stress response and heat shock proteins, suggesting that AS is not a random event, but rather a response related to stress. These results suggest that B. depauperata undergoes a complex loop in AS in adaptation to stress, whereas AS negatively regulates A. thaliana. Results from this study will help increase understanding of this complex loop of regulatory mechanisms and could lead to the engineering of crops that can withstand rising ambient temperatures.