Storage longevity of two contrasting recalcitrant seeded species was studied relative to oxidative metabolism and DNA damage under ambient storage (25 ± 2 °C, 50 ± 2% relative humidity). The present study was aimed to investigate the ageing-induced amendments in two recalcitrant seeded species, Madhuca latifolia and Shorea robusta. These are economically important tropical trees and are exploited extensively in commercial sectors. Fresh seeds of M. latifolia and S. robusta lost their germinability within 35 and 8 days after harvest, respectively, under ambient storage (temperature 25 ± 2 °C, relative humidity 50 ± 2%). To untangle the possible mechanisms involved in deteriorative changes in respective seeds, levels of reactive oxygen species (ROS) and changes in DNA content, oxidation, fragmentation and polymorphism, and DNase activity were monitored. The results revealed significant (2.1–7.3 folds) upsurge in ROS levels in these seeds. In contrast, remarkable fall in DNA content of embryonic axes (3.8 fold and twofold) and cotyledons (6.7 fold and twofold) of M. latifolia and S. robusta seeds, respectively, were observed. Moreover, enhanced oxidation (8.9–18.8 fold) and fragmentation (2.1–2.8 fold) of DNA along with increased (9.9–25.3 fold) DNase activity were observed in axes and cotyledons of respective seeds, revealing active participation of ROS in oxidation (r = 0.96, p < 0.05), and of DNase in fragmentation (r = 0.94, p < 0.05) of DNA. Dendrogram of RAPD unveiled significant alterations in similarity coefficients of aged and non-aged seeds of both the species. Thus, overall results concluded that loss of viability of M. latifolia and S. robusta seeds was closely associated with ageing related changes such as over accumulation of ROS, fall in DNA content, increased oxidation, fragmentation and DNA polymorphism, and DNase activity.