Natural regeneration depends on surviving propagules in the soil, seed sources from a surrounding landscape mosaic, and dispersal agents. We compiled and analyzed four sets of case studies varying in degree of disturbance, for secondary forests recovering from logging, fire, and conversion to agroforest in Sumatra or Kalimantan (Indonesia) on mineral and peat soils. Data on tree species diversity, wood density frequency distribution (indicative of successional status, databases with over 6000 species exist), and dispersal modes were compared with those for less disturbed comparator forests for the same landscapes. Undisturbed lowland dipterocarp forest in Kalimantan had close to 200 species of trees of more than 10 cm diameter at a 1 ha sample scale (and 450 at a 10-ha scale), regulation-based logging had little impact. Still, after the repeated fire a sample area of 2 ha was needed to reach the same species numbers. After forest conversion to low-management-intensity rubber agroforest, 50 tree species were found at a ha scale and close to 100 species in 3 ha. Peat swamp forest in Kalimantan and the Sumatra forest samples had close to 100 species in 1 to 2 ha. The Kalimantan forest after a repeated fire had a markedly higher fraction of low-wood-density trees (40%), but otherwise, all forests sampled were similar in overall wood density profiles. Logged-over forest managed by community (village forest) and rubber agroforest in Sumatra contained larger fractions of heavy-wood-density trees (including rubber). The majority of trees (50-70%) had birds, bats, and primates as dispersal agents in all sites. Logged-over forests on mineral soil had higher fractions of autochorous species (15%) compared to other sites. Anemochorous (wind-dispersed) species were most common (20%) in undisturbed lowland Dipterocarp forest and peat swamp forest recovering after logging and fire. Comparison between secondary forests and agroforests showed the influence of farmer selection regarding what is allowed to grow beyond the pole stage. Wood density and seed dispersal profile can be used as degradation indicators of species assemblages across various disturbance levels and types. They can also reflect the habitat quality of the surrounding forming restoration options.