ISEA fossils show super-archaic H. luzonensis and H. floresiensis present over 50,000 years ago when modern humans arrived. Modern ISEA populations have distinct Denisovan genomic ancestry from ancient interbreeding. Analysis of over 400 modern genomes including 200 from ISEA confirms widespread Denisovan introgression. No substantial super-archaic admixture signals detected in any genomes. Endemic ISEA super-archaic fossils incompatible with modern human genetic record. Denisovans genetically present in ISEA despite lacking local fossils. Super-archaic lineages did not contribute substantially to contemporary ISEA humans. Multiple Denisovan admixture pulses evident in some ISEA groups. Negritos and Papuans show deep Denisovan divergences. Fossil-genetic mismatch demands reevaluation of ISEA hominin history.