Sample preparation continues being a key factor to obtain fast and reliable quantification of Hg species. Assisted procedures enhance the efficiency and reduce the extraction time; however, collateral species transformations have been observed. Moreover, differential interconversions have been observed even between similar matrixes, which introduce an important uncertainty for real sample analysis. Trying to minimize Hg species transformations, we have tested a soft ultrasound-assisted extraction procedure. Species quantification and transformations have been evaluated using double spike isotope dilution analysis (IDA) together with gas chromatography inductively coupled plasma mass spectrometry (GC-ICP-MS) for a CRM material (Tort-2) and shark and swordfish muscle samples. Optimum extraction solution and sonication time led to quantitative extraction and accurate determination of MeHg and IHg in a short time, although different behaviors regarding species preservation were observed depending on the sample. Negligible species transformations were observed in the analysis of the CRM, while a small but significant demethylation factor was observed in the case of real samples. In comparison with other extraction procedures, species transformations became smaller, and fewer differences between fish species were found. Similar results were obtained for fresh and lyophilized samples of both fish samples, which permit one to analyze the fresh sample directly and save time in the sample preparation step. The high grade of species preservation and the affordability of the extraction procedure allow one to obtain accurate determinations even for routine laboratories using quantification techniques, which do not estimate species transformations.