Ultrasound (US) can modify the plant growth and development . Previous assessments of the transcriptome of in vitro potato (Solanum tuberosum L.) exposed to US transmitted through air (AB-US) or liquid (PE-US) revealed the up- or down-regulation of several stress-related differentially expressed genes (DEGs) related to abiotic stress . In a bid to better characterize stress-related elements over a four-week period, the transcriptome of AB-US was compared to that of PE-US . When comparing the controls of both treatments, DEGs related to hypoxia were not detected . Nevertheless, hypoxia-related DEGs were detected in the combination of liquid medium and ultrasonication . DEGs coding for chitinase, peroxidase, glutathione-S-transferase, transcription factors of ERF (ethylene responsive factor), DREB (dehydration-responsive element-binding), WRKY and MYB were also significantly highly expressed in PE-US, relative to AB-US . Up- and down-regulation of DEGs related to metabolic processes, and enzymes of the antioxidant system also confirm that PE-US is a more acute abiotic stress than AB-US . KEY MESSAGE: A transcriptomic analysis revealed that liquid-based ultrasonication was a stronger abiotic stressor than air-based ultrasonication . Of particular interest were the heat shock proteins and transcription factors in this comparison . Despite the ultrasound stress, explants survived and plantlets developed.