Among angiosperms, Cactaceae chloroplast genomes are one of the most variable in structure and gene content. Many groups have lost the inverted repeat regions (IR) and show gene inversions and deletions. The genus Mammillaria has a very variable plastome structure. So far, three different chloroplast genome structures have been identified in seven species. This variation could be useful in determining infrageneric relationships within Mammillaria. To test this, we assembled and analyzed four new chloroplast genomes of Mammillaria series Stylothelae. This series has been proposed based on the combination of morphological characters and by the lack of the rpl16 gene intron, which is present in all other Mammillaria species. It is unknown if the loss of rpl16 is from a single or recurring events, and further study of Mammillaria series Stylothelae may present novel instances of chloroplast genome structure variation. Here, we isolated chloroplasts, extracted DNA, and then sequenced it using Ion Torrrent sequencing with 200 base pair reads. Chloroplast genome contigs were de novo assembled using SPAdes. Then, we aligned them using the BWA program and evaluated the percentage of coverage versus the seven previously known plastomes to identify the most similar structure. The chloroplast genome of sampled species from Mammillaria series Stylothelae ranged from 100 to 103 kb. The number of genes varied from 97 to 99 with four to six pseudogenes. All plastomes exhibited a similar structure and gene content compared with Mammillaria pectinifera, but they were 6 to 8 kb shorter and lacked the IR regions. Furthermore, we detected the loss of some ndh genes in all the species. Using these new chloroplast genomes, we explore the extent of structural variation across Mammillaria. Our results support a high variation in the chloroplast genome of Mammillaria, which could be useful for phylogenetic inferences and to determine group boundaries.