Cryptococcus is a non-motile, gram positive, non-fermenting Basidiomycetous encapsulated yeast like fungus that causes respiratory, neurological and other systemic diseases in both humans and animals. Present study delineates the possible distribution of Cryptococcus species in pigeon droppings, excreta of other avian species, eucalyptus tree and contaminated soil specimens collected from different geographical co-ordinates of six geographical regions of the lower Brahmaputra Valley of Assam, India. The fungi were isolated through conventional methods of Sabouraud Dextrose Agar (SDA) and Bird Seed Agar (BSA) media and identified through negative staining of capsule as well as performing classical bio-chemical tests. Identity of the isolates was further confirmed through sequence analysis of ITS-1 and ITS-4 region of the 18S rDNA. Two pathogenic species of Cryptococcus were isolated from 67 (15.40%) of the 435 specimens. Of these positive isolates 41 (9.43%) belonged to Naganishia albida (Cryptococcus albidus) while 26 (5.98%) represented Papiliotrema laurentii (Cryptococcus laurentii). Both the species were recovered from 58 (18.35%) dry and 9 (7.56%) moist specimens. The percentage of prevalence of Naganishia albida in dry and moist specimens were 35 (11.07%) and 6 (5.04%) respectively. Contrary to this, the percentage of prevalence of Papiliotrema laurentii in dry and moist were 23 (7.28%) and 3 (2.52%) respectively. The findings indicate that Cryptococcus species have established a better ecological sustenance in dry specimens than moist. The findings of the investigation demonstrated that the prevalence of Cryptococcus albidus in attics, dovecotes / houses of pigeon fanciers, contaminated soil, eucalyptus tree and droppings of other birds were 11(12.36%) out of 89, 23(14.11%) of 163,2(3.23%) of 62,4(7.84%) of 51 and only 1(1.43%) out of 7 specimens respectively. The recovery of Papiliotrema laurentii in the above specimens were 3(3.37%), 20(12.27%), 1(1.61%), 1(1.96%) and 1(1.42%) respectively. The findings revealed that the prevalence of Naganishia albida is more than that of Papiliotrema laurentii in natural substrates. The notorious pathogenic fungi, Cryptococcus neoformans could not be isolated, indicative of the fact that the region selected for the study is not environmentally favorable for growth and sustenance of the species. Findings of the study clearly demonstrate the ecological and epidemiological significance of the non-neoformans species of the genus cryptococcus that needs further comprehensive studies to access the prevalence of the genus from public health point of view.