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She specialized in solar astronomy, and also discovered a number of comets, including periodic comet 45P/Honda-Mrkos-Pajdušáková, and the non-periodic C/1946 K1 (Pajdušáková-Rotbart-Weber), C/1948 E1 (Pajdušáková-Mrkos), C/1951 C1 (Pajdušáková) and C/1953 X1 (Pajdušáková).
She observed at Skalnaté Pleso Observatory and became its third director from 1958 to 1979.
She may have been married to Antonín Mrkos. In a 1951 "Comet Notes" article in Publications of the Astronomical Society of the Pacific [PASP 63 (1951) 209], Leland E. Cunningham in discussing comet C/1951 C1 refers to her as "Miss Pajdušáková (Mrs. Mrkos)", and there was an astronomy book published in 1956 by Ľudmila Mrkosová-Pajdušáková, as well as various scientific papers under this name from approximately 1952–1958. However, their respective biographies do not seem to mention any such marriage.
- "Zem tesne minula slovenská kométa" (in Slovak). hnonline.sk. 15 August 2011. Retrieved 9 December 2011.