Chironomid larvae have distinct salivary gland polytene chromosomes with precise banding patterns. Chromosome arms possess two transcriptionally active sites, i.e., Balbiani rings (BRs) and Nucleolar organizers (NORs). Structural changes in the chironomid chromosomes serve as pollution bioindicators in fresh water ecosystems, which are directly related to the ecology of the aquatic environment. Savar city is centrally located in Bangladesh and about 380,000 people live there, which makes it the second most populous city in the district. Anthropogenic sources, such as untreated industrial effluents, household waste, and run-off from agriculture, are the main reasons for surface and underground water pollution. Therefore, the aim of this study was to observe the polytene chromosome structural patterns of chironomid larvae collected from Savar wetland regions. Salivary gland polytene chromosomes of the 4^th instar larvae were examined in order to describe their chromosomal diversity in these habitats. We followed the lacto aceto orcein squash method for polytene chromosome preparation. Two karyotypes (Type 1 from Jahangirnagar Campus under Pseudothummi Cytocomplex and Type 2 from Savar DOHS under Thummi Cytocomplex) have been observed. Pseudothummi Cytocomplex has an AE, CD, BF, and G- chromosome arm combination, whereas Thummi cytocomplex shows an AB, CD, EF, and G- chromosome arm combination. Here, Thummi is considered to be basic, while Pseudothummi is considered to be structurally changed due to environmental factors. Chromosome arms BF and AB are the longest and G is the smallest in the karyotypes. In both types, BRs and NORs were detected in the G arms. Centromeric bands were also detected in each arm and these bands were deeply stained, i.e., were highly heterochromatic in nature. Karyotypic analysis in these two cytocomplexes has indicated the presence of a much larger chironomid fauna in this region, as well as structural changes in their chromosome arm combinations. Further research on the various structural rearrangements in the polytene chromosomes of chironomid larvae collected from polluted wetland water bodies is in progress.