The phylum Cryptista, as part of Diaphoretickes, shares a common ancestor with other early-diverging eukaryotic groups, including the Archaeplastida and the SAR supergroup (Stramenopiles, Alveolates, Rhizaria).

Classification of Palpitomonas has evolved over time as molecular phylogenetic has revealed its position as one of the earliest-diverging eukaryotic lineages, particularly among the flagellated protists.

Molecular phylogenetic analyses, particularly those involving ribosomal RNA (rRNA) sequences and protein-coding genes, have demonstrated that Palpitomonas is a basal lineage within Cryptista, with close related to the early-diverging mitochondrial ancestors of other eukaryotes.

[1][2][3] Phylogenetic analyses based on multigene datasets have shown Palpitomonas bilix as basal within the Cryptista clade, diverging before cryptophytes and katablepharids.

Palpitomonas is also part of broader studies that question the monophyly of Hacrobia, suggesting complex evolutionary relationships among early-diverging protists.

The anterior flagellum of Palpitomonas possesses mastigonemes—bipartite hair-like structures that aid in movement and feeding by creating a current that draws in food particles.

[1][4]Palpitomonas bilix has a distinctive mitochondrial genome, organized as a linear DNA molecule with large inverted repeats at both ends.

[2][1] Palpitomonas play an ecological role in marine environment, as a bacterivore by consuming bacteria provide the regulation of bacterial populations and helping in nutrient cycling within microbial communities.

[1] The combination of basal features in Palpitomonas, such as its linear mitochondrial genome and ancestral cytochrome c maturation system, make it an important organism for understanding evolutionary in eukaryotes.

Position within Cryptista and Hacrobia and its early diverging lineage provide insights into the development of mitochondria, cellular structures, and other eukaryotic traits.