Galdieria sulphuraria stands out among the unicellular alga owing to its versatile characteristics, such as, survival on different carbon media and adaptation to extreme or hostile environments, namely, high heat, heavy-metal-toxic, and high acidity. The environmental adaptation has been attributed to the bacterial and archaeal genes that were acquired by G. sulphuraria during the course of its evolution. Previous studies reported ~5% of the G. sulphuraria genes to have been acquired through horizontal gene transfer. This was considered a conservative estimate, and the contribution of gene transfer to the extremophily of this organism is not yet well-understood, primarily because of the lack of the sequenced genomes of its close relatives. To circumvent the limitations of the current comparative genomics methods that require a rich sampling of the related genomes for a reliable inference of “alien” genes, we adapted a “comparison-free” method that had earlier been applied to assess the impact of horizontal gene transfer on the evolution of prokaryotes. We first analyzed the genome of G. sulphuraria for the presence of compositionally atypical genes using an integrated recursive segmentation and agglomerative clustering method. The clusters of compositionally homogeneous segments generated by this method revealed that ~30% of G. sulphuraria genome harbors atypical genes. The genes found in these regions were further assessed using pairwise sequence alignment of their protein products with protein sequences in the databases. A subset of predicted atypical genes (~15% of the G. sulphuraria genes) were found to have closest similarities with bacterial and/or archaeal genes but not the algal genes. The potential donor organisms, mostly proteobacteria and archaea, are known to thrive in various hostile conditions, and possess genes for the metabolism of various toxic elements. Our study reveals many, yet unreported, alien genes, documenting frequent transfer of genes from different prokaryotes to an extremophile eukaryote.