Shifting malaria species composition amid declining transmission in India: longitudinal evidence from 27 states, 2009–2019

India has made substantial progress towards malaria elimination, although national declines may conceal substantial heterogeneity in parasite composition across geographic settings. We analysed monthly state-level Health Management Information System (HMIS) records from April 2009 to December 2019 across 27 Indian states with complete observations. For the analytical dataset, total malaria-positive cases were defined as the sum of Plasmodium falciparum and Plasmodium vivax positive cases. Beta-binomial mixed-effects models were used to examine temporal and seasonal changes in malaria positivity and parasite composition, with state-specific temporal effects used to assess heterogeneity in species-composition trajectories across states. Adjusted total malaria positivity declined from 3.14% (95% CI: 2.30–4.28) in 2009 to 0.94% (0.68–1.30) in 2019, despite a 60.1% increase in blood smears examined. P. falciparum positivity declined from 1.14% to 0.40%, while P. vivax positivity declined from 1.67% to 0.48%. Despite declines in positivity for both species, there was no significant overall temporal change in the relative contribution of P. falciparum (OR: 0.995; 95% CI: 0.985–1.005; p = 0.304), while state-specific trajectories differed markedly (likelihood-ratio χ 2 = 1435.7, df = 2; p < 0.001), with the P. falciparum share declining in six states and increasing in Karnataka and Tripura. Seasonal variation also persisted, although the timing of peak malaria positivity varied considerably across states, ranging from February to December. These findings indicate that India's declining malaria burden masks substantial geographic heterogeneity in parasite composition and seasonal transmission. As elimination approaches, identifying where, when and which parasite species persist may provide additional epidemiological information for strengthening geographically and seasonally responsive malaria surveillance and control efforts.