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Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds—<i>Calidris canutus</i>, <i>Jacana jacana</i>, and <i>Vanellus chilensis</i>—combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10–28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in <i>C</i>. <i>canutus,</i> we found two microchromosomes involved in chromosome fusions, they were present as single pairs in <i>V</i>. <i>chilensis</i>. We also described a new chromosome number for <i>C</i>. <i>canutus</i> (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species.