Morphology, morphogenesis and molecular phylogeny of a freshwater oxytrichid ciliate, Aponotohymena isoaustralis n. sp. collected from Sanjay Lake (28°36′51″N, 77°18′14″E), Delhi, India, were studied. The described species is characterized by a flexible body, with body size (in vivo) of about 148 × 46 µm and yellowish green cortical granules. Morphological characters exhibit: undulating membranes in Notohymena–pattern; two macronuclei and absence of micronucleus (amicronucleate); about 36 adoral membranelles; 18 frontoventral-transverse (FVT) cirri; one right and one left marginal row separated posteriorly; 6 dorsal rows; 7 caudal cirri arranged in 2 + 2 + 3 pattern (constant). In the present study, a detailed description of all the developmental stages is also provided. Prominent distinguishing features of the new species are the absence of micronucleus, 7 caudal cirri (constant), yellowish green cortical granules aligned along the margins and irregularly distributed throughout the cell. They may also be randomly concentrated as clusters along the left margin and posterior end of the cell. Molecular phylogeny based on small subunit rDNA sequence data suggests sister relationship of Aponotohymena isoaustralis n. sp. with Notohymena apoaustralis and Aponotohymena australis (Notohymena australis) which cluster in a clade with Paraurostyla weissei and Paraurostyla coronata. Further analysis of nucleotide sequence of SSU rDNA also suggests that A. isoaustralis n. sp. is distinct from the type species A. australis.
