In tropical coastal ecosystems mangrove forests are important as feeding, spawning, breeding and nursery grounds for many marine species. High human population pressure in coastal areas has led to the loss and deterioration of mangrove habitats. Solar salt production can affect these habitats along the East African coast. Littorinid snails live on mangrove trees, forming an important component of the mangrove ecosystem and have been used as bioindicators of environmental health and community stress. Littoraria subvittata is the most abundant littorinid species in mangroves along the East African coast. Partial mitochondrial cytochrome oxidase subunit 1 (COI) gene sequences of 298 individuals were used to assess the impact of mangrove deforestation at salt ponds on the genetic diversity and structuring of L. subvittata populations, as well as to infer the demographic history of the species. Nucleotide and haplotype diversities were found to be lower in samples from mangroves at salt ponds than in samples from natural mangroves. The mean nucleotide diversity was 0.049 ± 0.036% and 0.115 ± 0.068% in mangroves at salt ponds and natural mangroves, respectively. The mean haplotype diversity was 0.23 ± 0.14 and 0.50 ± 0.14 in mangroves at salt ponds and natural mangroves, respectively. Analysis of molecular variance (AMOVA) detected a significant population structure (Фst = 0.049; P < 0.0001) for the combined populations. Hierarchical AMOVA detected a significant population genetic structure only between populations from mangroves at salt ponds and natural mangroves (Φct = 0.022; P < 0.05), but not between any other groupings. Populations from natural mangrove sites showed a significant genetic structure (Фst = 0.054, P < 0.0001), while populations from sites at salt ponds could not be differentiated (Фst = −0.0026, P = 0.64). Reduced effective population size was observed in most samples from mangrove sites at salt ponds compared with natural mangrove. The direction of migrants was mostly from salt ponds to natural mangroves. These results show that salt ponds have a negative impact on the genetic diversity of L. subvittata populations and modify the population's genetic structure.