For too long, humans have been in the battle for combating malaria, and today it is still a massive public health burden. Efforts in the past have rendered some success but now seem under threat with evidence of stagnation. More troublesome, to this day, 93% of all malaria deaths happen in sub-Saharan Africa, which holds the highest malaria burden in the world. Numerous aspects (epidemiological, social, ecological and economical) need to come together as a front in order to finally eradicate malaria.  Malaria is transmitted through the bite of an Anopheles female mosquito, and two species complexes are largely responsible for the intense malaria transmission in the continent of Africa: Anopheles gambiae and Anopheles funestus. These complexes are characterized by the presence of inversion polymorphisms, a phenomenon where a chromosomal segment breaks and reattaches in reverse orientation. Inversion polymorphisms can suppress recombination between alternative arrangements in heterokaryotpes, making it possible to maintain groups of alleles within breakpoints. They are thought to confer beneficial traits to the mosquitoes, allowing their carriers to distribute widely across a plethora of environments. Here, we focus on two sister species of the Anopheles gambiae complex: Anopheles gambiae s.s. and Anopheles coluzzii. The two are among the most widely spread and efficient vectors.  A lot of what we know about inversions today was possible due to intensive cytogenetic karyotyping, a method widely accepted but limiting in the sense that it is life stage and sex specific. Evidence suggests that inversions are related to epidemiological relevant traits (plasmodium infection rate, indoor/outdoor resting and biting behavior). Understanding the presence of inversion polymorphism in the complex will not only facilitate characterization of these species but will advance the understanding of malaria transmission. We can no longer rely on inversion blind vector control approaches. Recognizing that malaria is not only a health burden but an economic one, we present here cost-effective assays to molecularly karyotype inversion polymorphisms for two inversions in the right arm of chromosome 2. By using a group of recently identified single nucleotide polymorphisms (SNPs) that correlate with inversion status, we have created polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) assays. The assays augment the limited but accepted cytogenetic karyotyping method, therefore advancing the study of the role of inversions.