Partial small subunit ribosomal DNA (SSU rDNA) sequence analysis was used to determine the phylogenetic position and genetic diversity of the arborescent agglutinated foraminifer Notodendrodes hyalinosphaira. Our results show that N. hyalinosphaira is closely related to N. antarctikos, a co-occurring arborescent species. In all phylogenetic analyses employed, both species branched within a well-defined group. No sequence variations were observed within either species. However, molecular examination of different infaunal “quartz sphere” morphotypes attributed to N. hyalinosphaira, among others, reveals the presence of two distinct genotypes which may represent as yet undescribed ancestors of Notodendrodes.