1. Ecosystem retrogression occurs during the very long-term absence of major disturbances, and it is characterized by decreases in productivity, decomposition rates and nutrient availability. Ratios of total soil nitrogen (N) to phosphorus (P) also characteristically increase during retrogression, but the nature of N inputs to ecosystems undergoing retrogression has seldom been explored. 2. We studied a 5000-year-old chronosequence involving 30 islands that differed greatly in history of disturbance (wildfire through lightning strike), with increasing time since disturbance leading to ecosystem retrogression. For each island, we quantified N inputs through biological fixation by cyanobacteria hosted by each of two feather moss species that dominate the ground layer vegetation (Pleurozium schreberi and Hylocomium splendens), and compared these with N inputs through atmospheric deposition. 3. Both N2 fixation per unit land area and fixation per unit moss mass increased significantly with increasing time since disturbance for both moss species. As retrogression progressed, the amount of total N input through biological fixation increased to levels comparable to that of input through atmospheric deposition. 4. Across the chronosequence, N has been accumulating in the humus layer at a rate of 1.8 kg ha-1 year-1 in the absence of fire during the past 5000 years. The added N input from biological fixation in this area of low atmospheric N deposition helps explain this relatively high rate of sequestration. 5. Our results show that, contrary to several claims in the literature, biological N2 fixation is not only important in early-successional ecosystems but also in late-successional systems that have undergone retrogression. This fixation can contribute both to the elevated N : P ratios that occur during retrogression and to accumulation of N capital in the soil. However, much of this N may exist in forms that are relatively unavailable to co-existing plant species.