Two varieties of Saxifraga diversifolia, diversifolia and parnassifolia, collected from the moist alpine slopes around Gauri Kund, 3930 m (Manimahesh Hills, Himachal Pradesh, India), are studied for detailed male meiosis, chiasma frequency and pollen fertility. Both varieties exist at diploid level (based on x = 8), and show a meiotic chromosome count of n = 8 at diakinesis and metaphase-I, and regular chromosome distributions at anaphases-I/II. The meiotic chromosome count of n = 8 ascertained here represents a new aneuploid cytotype, supplementing the earlier report of a diploid cytotype with 2n = 20 from the north-west Himalayas in India and the Nepal Himalayas. Of the two varieties, var. diversifolia showed the presence of multiple chromosomal associations and univalent chromosomes at diakinesis and metaphase-I of meiosis-I. On the other hand, var. parnassifolia does not have multivalent formation but showed only 2–4 univalent chromosomes at diakinesis and metaphase-I. Occurrence of univalents in pollen mother cells of var. diversifolia and parnassifolia reduced the chiasma frequency significantly and also caused some pollen sterility (7–8%). The paper herein discusses for the first time the occurrence of structural heterozygosity and univalent chromosomes and their apparent affect on chiasma frequency and pollen fertility in S. diversifolia.