When learning the phonological categories of a second language (L2), learners have to deal with phonetic variation. For instance, allophonic variant forms have to be recognized as the same phoneme. A minimal pair identification task was used to assess how late Spanish learners of German perceive the phonological /r/-/h/ contrast. German /r/ was realized as one of three allophones ([r], [R], [K]) that vary in phonetic similarity to /h/ as well as to the typical phonetic form of Spanish /r/ (i.e., [r]). Results showed that learners were very good at identifying all German variant forms (>90% correct). However, [K], which is phonetically closest to German /h/ and furthest from Spanish /r/, was identified significantly worse than [r] and [R]. Relating these results to a cross-language perception task where learners were asked to map the German allophones of /r/ and the phoneme /h/ to different L1 phonological categories further showed that those learners were best at identifying words with [K] who consistently matched it to a single L1 category. Surprisingly this category did not always have to be the phonologically matching Spanish /r/. We conclude that phonological and phonetic relations between the learners' L1 and L2 are important in identifying allophones of the same L2 category.

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