Mondell pine (Pinus eldarica Medw.) is a rare and drought resistant pine, found naturally only in semi desert environment southeast of Tbilisi, Georgia, and has been probably introduced to Iran more than 800 years ago. This species has gradually altered both in shape and growth rate in Nashtifan‐Khaf, and generated two species nova which so called as ball shaped and conical, according to characteristics of their shape and smaller stature. This study was conducted to discriminate these species nova using epicuticular wax features and certain biochemical characteristics i.e., peroxidase electrophoretic pattern (PAGE), the activity of soluble (SPO), ionically (IPO) and covalently (CPO) wall‐bound fractions of peroxidase, lignin and total protein content. Observation via scanning electron microspopy showed differences that in adaxial and abaxial surface of needles, and also seed surface, in ball shaped type with the others. But none of the biochemical characteristics had significant difference in these three types. The electrophoretic analysis showed that the peroxidase isozyme is not suitable marker for discriminating the species nova from wild type, in spite of obvious micro‐ and macromorphological differences. Results of current study, propose the use of molecular markers and cytogenetic studies in order to specify cause of species nova occurrence in the study area. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)