Hepatocellular carcinoma (HCC) remains a global health challenge with high mortality rates, largely due to late diagnosis and suboptimal efficacy of current therapies. With the imperative need for more reliable, non-invasive diagnostic tools and novel therapeutic strategies, this study focuses on the discovery and application of novel genetic biomarkers for HCC using explainable artificial intelligence (XAI). Despite advances in HCC research, current biomarkers like Alpha-fetoprotein (AFP) exhibit limitations in sensitivity and specificity, necessitating a shift towards more precise and reliable markers. This paper presents an innovative XAI framework to identify and validate key genetic biomarkers for HCC prognosis. Our methodology involved analyzing clinical and gene expression data to identify potential biomarkers with prognostic significance. The study utilized robust AI models validated against extensive gene expression datasets, demonstrating not only the predictive accuracy but also the clinical relevance of the identified biomarkers through explainable metrics. The findings highlight the importance of biomarkers such as TOP3B, SSBP3, and COX7A2L, which were consistently influential across multiple models, suggesting their role in improving the predictive accuracy for HCC prognosis beyond AFP. Notably, the study also emphasizes the relevance of these biomarkers to the Hispanic population, aligning with the larger goal of demographic-specific research. The application of XAI in biomarker discovery represents a significant advancement in HCC research, offering a more nuanced understanding of the disease and laying the groundwork for improved diagnostic and therapeutic strategies.