Understanding microsite requirements is critical for restoring sustainable rare plant populations and creating meaningful management plans that will enhance native species’ population viability. Natural areas bordered by urban communities have restricted size and constrained management options that confound goals of preserving biodiversity. Using geographical information systems and observational and experimental studies, we determined that current microsites required for seedling establishment within existing habitat of the federally endangered Crenulate leadplant are few and spatially restricted, resulting in little wild seedling recruitment. Experimental and wild seedlings had highest germination rates in litter layers 1–2 cm in depth and survived the longest in litter 0.5–2 cm deep. Fire suppression and aggressive native and exotic plants have accumulated litter up to 33 cm near some of the wild adult Crenulate leadplant. Only 9% of habitat occupied by this taxon at its largest population is conducive to seedling establishment. Similarly, 30% is conducive to seedling establishment in the second largest population. Fire plays a critical role in South Florida ecosystem dynamics and the restoration and preservation of its landscape and biodiversity. When fire is not possible, other management is needed. Manual litter and downed debris removal are recommended at both population sites to improve the probability of Crenulate leadplant seedling establishment and population persistence.