Due to its unique combination of high elevation and climate, the Alakaʻi Swamp harbors a large number of endangered endemic species that are only found in this area and whose population has been dramatically declining over the last decades.

Habitat loss and diseases carried by introduced mosquitoes (in particular avian malaria and avipoxvirus) have decimated the endemic bird population and further restricted their range.

The study concluded that, of these three ecosystems, the Alakaʻi Swamp "offers the least hope for maintaining endemic honeycreepers in the face of malaria and climate change".

Notable species of endemic plants that are federally endangered and are found in the area include: Introduced species found in the area include: gold fern (Pityrogramma calomelanos), a type of sedge (Mariscus meyenianus), broadleaf rush (Juncus planifolius), narrow-leaved carpetgrass (Axonopus fissifoilius), vasey grass (Paspalum urvillei), Glenwood grass, (Sacciolepis indica), broomsedge (Andropogon virginicus), Kahili ginger (Hedychium gardnerianum), montbretia (Crocosmia × crocosmiiflora), firetree (Myrica faya), prickly Florida blackberry (Rubus argutus), thimbleberry (Rubus rosifolius), fireweed (Erechtites valerianifolia), and hairy cat's ear (Hypochoeris radicata).

The State of Hawaii Parks Division built an extensive boardwalk along most of the trail and elevated above the swamp as a measure to protect this highly sensitive habitat.